id float64 1.55k 110k ⌀ | title stringlengths 1 256 ⌀ | template_id float64 0 6 ⌀ | doi stringlengths 39 49 ⌀ | url stringlengths 40 92 ⌀ | authors stringlengths 1 933 ⌀ | protocol_text stringlengths 34 1.08M | steps_list stringlengths 2 269k |
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79,540 | Plasmid-reprogramming of human fibroblasts | 4 | dx.doi.org/10.17504/protocols.io.5qpvor45bv4o/v1 | https://www.protocols.io/view/plasmid-reprogramming-of-human-fibroblasts-crwuv7ew | Pascale Baden, michela.deleidi | TITLE: Plasmid-reprogramming of human fibroblasts
AUTHORS: Pascale Baden, michela.deleidi
[DESCRIPTION]
This protocol details about plasmid-reprogramming of human fibroblasts.
[GUIDELINES]
Adapted from Okita et al PMID: 21460823.
[STEPS]
SECTION: Nucleofection (Day 0)- with Amaxa Nucleofector I/II
1. Prepare nucleof... | ["[Nucleofection (Day 0)- with Amaxa Nucleofector I/II] Prepare nucleofection solution: \n Human Dermal Fibroblast Nucleofector solution 82 µL Supplement 18 µl Plasmid 10 µg", "[Nucleofection (Day 0)- with Amaxa Nucleofector I/II] Nucleofect 700.000 fibroblasts (resuspended in the nucleofection soluti... |
76,758 | Lactate Concentration assay (LDH method) | 4 | dx.doi.org/10.17504/protocols.io.6qpvr4733gmk/v1 | https://www.protocols.io/view/lactate-concentration-assay-ldh-method-cn7wvhpe | Daniel T Hass, James Hurley | TITLE: Lactate Concentration assay (LDH method)
AUTHORS: Daniel T Hass, James Hurley
[DESCRIPTION]
The assay I describe measures lactate concentration in a sample. The principle of the assay is to convert lactate in a sample and excess NAD+ in the buffer to pyruvate and NADH with lactic dehydrogenase. Pyruvate is trap... | ["[Generate lactate standards] Make a lactate stock solution (for me, normally 1 M), and dilute to make standards. My typical standards are 0-20 mM (20, 16, 12, 8, 6, 4, 2, 1, 0.5, 0 mM). The composition of standards may of course be adapted to your needs. \n\nNote:\nThe range of the standard curve must exceed the rang... |
null | null | null | dx.doi.org/10.17504/protocols.io.d8a9sd | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<span style="color: #333333; font-family: 'Helvetica Neue', Helvetica, Arial, sans-serif; font-size: 14px;">A collection of tutorials for the VIROME application. <br /><br />Wommack, K. E., J. Bhavsar, S. W. Polson, J. Chen, M. Dumas, S. Srinivasiah, M. Furman, S. Jamindar, and ... | [] |
74,066 | UPitt TriState SenNet TMC Cell Hashing of single cell suspension for scRNAseq in 5' workflow (10x Genomics) | 4 | dx.doi.org/10.17504/protocols.io.36wgqjdy5vk5/v1 | https://www.protocols.io/view/upitt-tristate-sennet-tmc-cell-hashing-of-single-c-ckjsuune | Tracy Tabib, Oliver Eickelberg, koenigshoffm, Robert Lafyatis | TITLE: UPitt TriState SenNet TMC Cell Hashing of single cell suspension for scRNAseq in 5' workflow (10x Genomics)
AUTHORS: Tracy Tabib, Oliver Eickelberg, koenigshoffm, Robert Lafyatis
[DESCRIPTION]
TotalSeq™-C antibodies can be used for Cell Hashing in the 5' workflow, and can be purchased from BioLegend directl... | ["[Antibody Mix Supernatant Preparation] Buffers – Preparation\nFor samples containing >70% viable cells \n • Chilled (4°C): PBS + 1% BSA \n • Chilled (4°C): PBS + 0.04% BSA \nFor samples containing <70% viable cells \n • Chilled (4°C): PBS + 10% FBS", "[Antibody Mix Supernatant Preparation] Prepare Antibody M... |
69,841 | 城市微生物相調查計畫—採集土壤教學 | 1 | dx.doi.org/10.17504/protocols.io.4r3l2oxzpv1y/v4 | https://www.protocols.io/view/protocol-cgfrttm6 | Hsin-Mao Wu | TITLE: 城市微生物相調查計畫—採集土壤教學
AUTHORS: Hsin-Mao Wu
[DESCRIPTION]
吳昕懋
[STEPS]
SECTION: 採土與iNaturalist紀錄教學
1. 移除表土，取距離土表5~7公分之處的土，裝入塑膠夾鏈袋中
SECTION: 採土與iNaturalist紀錄教學
2. 將塑膠袋中的土均勻混合，倒入採集罐之中
SECTION: 採土與iNaturalist紀錄教學
3. 在採集紀錄紙上勾選採樣地點、採樣種類，以及填寫日期、城市、鄉鎮、地點、採集者等資訊
SECTION: 採土與iNaturalist紀錄教學
4. 最後拍兩張照片
... | ["[採土與iNaturalist紀錄教學] 移除表土，取距離土表5~7公分之處的土，裝入塑膠夾鏈袋中", "[採土與iNaturalist紀錄教學] 將塑膠袋中的土均勻混合，倒入採集罐之中", "[採土與iNaturalist紀錄教學] 在採集紀錄紙上勾選採樣地點、採樣種類，以及填寫日期、城市、鄉鎮、地點、採集者等資訊", "[採土與iNaturalist紀錄教學] 最後拍兩張照片", "[採土與iNaturalist紀錄教學] 接著打開iNaturalist app", "[採土與iNaturalist紀錄教學] 如圖所示，點選右下角的加號", "[採土與iNaturalist紀錄教學] 如下圖所示接著需選擇觀察類型，請點「選擇... |
10,323 | Chloroquine agarose gel | 1 | dx.doi.org/10.17504/protocols.io.nbtdann | https://www.protocols.io/view/chloroquine-agarose-gel-nbtdann | Salima Rüdiger, Anne Rediger, Rainer Machne | TITLE: Chloroquine agarose gel
AUTHORS: Salima Rüdiger, Anne Rediger, Rainer Machne
[DESCRIPTION]
DNA is not only separated by size, but also by conformation. This can be used as advantage when it comes to separate and visualize topoisomers of the same plasmid: the more supercoiled a plasmid, the more compact it is.... | ["[Preparing a fresh 1.2% agarose gel] A 1.2% agarose gel consists of:\n \n2.7 g agarose \n225 ml 0.5x TBE \n\n\nMix both together in an open 500 ml bottle and boil it up in a microwave. The agarose should be dissolved and the hot solution completely clear.\n \nMix the solution with putting it on a magnetic stirrer wit... |
17,455 | Modified Dixon’s Agar (Heitman Lab) | 1 | dx.doi.org/10.17504/protocols.io.q26g7rp11vwz/v1 | https://www.protocols.click/view/modified-dixon-s-agar-heitman-lab-vape2dn | Heitman Lab, Amy Gladfelter | TITLE: Modified Dixon’s Agar (Heitman Lab)
AUTHORS: Heitman Lab, Amy Gladfelter
[DESCRIPTION]
Media recipe for growth of Malassezia species.
[STEPS]
1. Malt extract . 36 g
2. Mycological peptone (Oxoid L40) 10 g
3. Dessicated ox bile (Oxoid) . 10 g
4. Agar 20 g
5. Tween 60 (heated before use) 10 mL
6. Glycerol,... | ["Malt extract . 36 g", "Mycological peptone (Oxoid L40) 10 g", "Dessicated ox bile (Oxoid) . 10 g", "Agar 20 g", "Tween 60 (heated before use) 10 mL", "Glycerol, 50% 4 mL", "dH2O 986 mL", "Sterilize by autoclaving at 121 °C for 15 min.", "Cool to 50 °C."] |
82,032 | Bleach/Sync Large Scale Culture Plates (LSCP) | 4 | dx.doi.org/10.17504/protocols.io.kxygx9jnkg8j/v1 | https://www.protocols.io/view/bleach-sync-large-scale-culture-plates-lscp-cucqwsvw | Muhammad Zaka Asif, Man Shah | TITLE: Bleach/Sync Large Scale Culture Plates (LSCP)
AUTHORS: Muhammad Zaka Asif, Man Shah
[DESCRIPTION]
This abstract describes how to bleach/synchronize a large mixed-stage population of C. elegans grown on Large Scale Culture Plates (LSCP). For more information on LSCPs, refer to Shaver et al., 2021.
[STEPS]
1. W... | ["Wash LSCP with 50mL M9, Centrifuge and aspirate the supernatant from the wash 15 mL at a time (it should take about 3 centrifuges since some of the buffer will soak into the agar or be irrecoverable).", "Repeat the 50 mL washes 2 more times for a total of 3 washes. (Shaver et al., 2021)", "Centrifuge the flip top tub... |
null | null | null | dx.doi.org/10.17504/protocols.io.pundnve | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?. | [] |
42,215 | Immunohistochemical staining of CD44 core proteins in islet beta cells of formalin-fixed mouse pancreas | 1 | dx.doi.org/10.17504/protocols.io.bmgfk3tn | https://www.protocols.io/view/immunohistochemical-staining-of-cd44-core-proteins-bmgfk3tn | Lora Starrs, Debra Brown, Sarah Popp, Charmaine Simeonovic | TITLE: Immunohistochemical staining of CD44 core proteins in islet beta cells of formalin-fixed mouse pancreas
AUTHORS: Lora Starrs, Debra Brown, Sarah Popp, Charmaine Simeonovic
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify">Paraffin sections (4m... | ["See Guidelines before starting", "Deparaffinize slides in each xylene for 1 min. rehydrate slides in graded alcohols beginning in absolute ethanol (10 dips)/ container of absolute ethanol), followed by 90% ethanol (10 dips) and 70% ethanol (10 dips).Wash well in running tap water for 5 min.", "Wipe around sections wi... |
11,436 | Arabidopsis flower dip transformation | null | dx.doi.org/10.17504/protocols.io.pekdjcw | null | Magdalena Julkowska | TITLE: Arabidopsis flower dip transformation
AUTHORS: Magdalena Julkowska
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A standard protocol how to transform Arabidopsis plants using a flower-dip method.
</div><div class = "text-block"> For higher rates of transformation, plants may be dipped tw... | ["Grow healthy Arabidopsis plants until they are flowering.", "Prepare Agrobacterium tumefaciens strain carrying gene of interest on a binary vector. Grow a large liquid culture @ 28C in LB with antibiotics to select for the binary plasmid, or grow in other media.", "Spin down Agrobacterium, resuspend to OD600 = 0.8-1.... |
100,085 | MyHC-IIb/Laminin Fresh Frozen | 0 | null | https://www.protocols.io/view/myhc-iib-laminin-fresh-frozen-ddyv27w6 | Griffen Wakelin | TITLE: MyHC-IIb/Laminin Fresh Frozen
AUTHORS: Griffen Wakelin
[DESCRIPTION]
Myosin heavy chain IIb/laminin immunofluorescence staining protocol for fresh frozen skeletal muscle.
[STEPS]
SECTION: Staining
1. Thaw sections, dry for ~30 mins, pap, and label.
SECTION: Staining
2. Block 60 min Room temperature
SEC... | ["[Staining] Thaw sections, dry for ~30 mins, pap, and label.", "[Staining] Block 60 min Room temperature", "[Staining] Wash 1X PBS 5 min", "[Staining] Wash 1X PBS 5 min", "[Staining] Wash 1X PBS 5 min", "[Staining] Incubate primaries in 1% BSA:\n 1:10\n 1:1000\n 4 °C", "[Staining] Wash 1X PBS 5 min", "[Staining] ... |
23,016 | Mouse Stellate Immunohistochemistry protocol | null | dx.doi.org/10.17504/protocols.io.2qggdtw | null | Pradeep Rajendran | TITLE: Mouse Stellate Immunohistochemistry protocol
AUTHORS: Pradeep Rajendran
[STEPS]
?. See mouse steallte isolation protocol
?. Complete/intact stellate ganglia are fixed in 4% paraformaldehyde overnight at 4oC.
?. Fixed tissue is rinsed in phosphate buffered saline (PBS), and stored in PBS + 0.02% sodium azide.
?.... | ["See mouse steallte isolation protocol", "Complete/intact stellate ganglia are fixed in 4% paraformaldehyde overnight at 4oC.", "Fixed tissue is rinsed in phosphate buffered saline (PBS), and stored in PBS + 0.02% sodium azide.", "The stellate ganglion whole mounts are permeabilized in 'block' solution. (10% normal do... |
null | null | null | dx.doi.org/10.17504/protocols.io.qbddsi6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is a two-part lipid extraction for labyrinthulomycetes. The only strain we have tried this protocol on so far is <em>Aurantiochytrium limacinum</em> ATCC MYA-1381.</p>
<p> </p>
<p>This protocol was modified from: Higgins, B.T., A. Thornton-Dunwoody, J.M. Labavit... | [] |
50,413 | Cell culture, transfection and imaging | 1 | dx.doi.org/10.17504/protocols.io.bvgmn3u6 | https://www.protocols.io/view/cell-culture-transfection-and-imaging-bvgmn3u6 | Marianna Leonzino, Andrés Guillén-Samander, Pietro De Camilli | TITLE: Cell culture, transfection and imaging
AUTHORS: Marianna Leonzino, Andrés Guillén-Samander, Pietro De Camilli
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol details the general preparation of cells for imaging and also for imaging experiments involving cellular hypotonic ... | ["[General preparation]\nCulture the COS-7 or HeLa (ATCC) cells at and 5% CO2 in DMEM containing 10% FBS, sodium pyruvate, penicillin, streptomycin and L-glutamine (all from Gibco).\n37 °C\n100\nNote: For general maintenance, when cells reached 80-90% confluency, they were deattached from the dish with Trypsin and... |
null | null | null | dx.doi.org/10.17504/protocols.io.duw6xd | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is part of the <a href="https://www.protocols.io/view/HERP-Haploid-Engineering-and-Replacement-Protocol-drq55v" target="_blank">HERP protocol</a>, from: <br /> <span class="cit-auth cit-auth-type-author">Alexander WG</span> <span class="cit-sep cit-sep-separator">, </span> ... | [] |
88,517 | Electrospray ionization analysis of eluted nucleotides | 4 | null | https://www.protocols.io/view/electrospray-ionization-analysis-of-eluted-nucleot-c2pdydi6 | Annan SI Cook, Xuefeng Ren, Anthony T. Iavarone | TITLE: Electrospray ionization analysis of eluted nucleotides
AUTHORS: Annan SI Cook, Xuefeng Ren, Anthony T. Iavarone
[DESCRIPTION]
This protocol describes the denaturation of PI3KC3-C1, and subsequent analysis of eluted nucleotides by electrospray ionization mass spec.
[STEPS]
SECTION: Buffer Exchange
1. Wash a 5 ... | ["[Buffer Exchange] Wash a 5 mL desalting (PD-10) column with 0.5 Molarity (M) NH4CH3CO2.", "[Buffer Exchange] Load PI3KC3-C1(VPS15-TSF) and PI3KC3-C1(mCherry-ATG14|VPS15-TSF) protein samples onto a 5-mL PD-10 column.", "[Buffer Exchange] Exchange the protein sample buffer by passing the protein through the column.", "... |
41,291 | microfluidic sars cov 2 lamp protocol | 4 | dx.doi.org/10.17504/protocols.io.bkjjkukn | https://www.protocols.io/view/microfluidic-sars-cov-2-lamp-protocol-bkjjkukn | Monica Simion, Alexandru Salceanu | TITLE: microfluidic sars cov 2 lamp protocol
AUTHORS: Monica Simion, Alexandru Salceanu
[STEPS]
?. [LAMP Amplification]
LAMP Colorimeteric AmplificationAdd of Add ofAdd ofAdd of product from step 1Incubate for at Read the colour of the reaction mix
12.5 µl
2.5 µl
8 µl
2 µl
65 °C
Red - SARS Cov 2 - negativeYellow-... | ["[LAMP Amplification]\nLAMP Colorimeteric AmplificationAdd of Add ofAdd ofAdd of product from step 1Incubate for at Read the colour of the reaction mix\n12.5 µl\n2.5 µl\n8 µl\n2 µl\n65 °C\nRed - SARS Cov 2 - negativeYellow- SARS Cov2 - positive", "[LAMP Amplification]\nMIX saliva in 1x TE bufferAdd ofand mix wi... |
72,736 | Skin Biopsy Protocol (Mammals): Non-lethal Sampling | 1 | null | https://www.protocols.io/view/skin-biopsy-protocol-mammals-non-lethal-sampling-ci98uh9w | sanaz.arenivas, justin_bohling, comizzolip, mhouck, racheljohnston, Jacquelyn Mountcastle, Budhan Pukazhenthi, phil.purdy, brian_small, seth_willey | TITLE: Skin Biopsy Protocol (Mammals): Non-lethal Sampling
AUTHORS: sanaz.arenivas, justin_bohling, comizzolip, mhouck, racheljohnston, Jacquelyn Mountcastle, Budhan Pukazhenthi, phil.purdy, brian_small, seth_willey
[DESCRIPTION]
Version date: 15 November 2022
The following protocol illustrates how to collect and shi... | ["[Preparation] Pre-chill icepacks in the freezer the day before planning to collect and ship samples.", "[Preparation] Record all information indicated in the biopsy form, including a picture of the animal for identification and GPS location where the animal was found.", "[Preparation] For general sedation, anesthetiz... |
72,888 | Intelligent Job and Career Recommender Systems: A Systematic Review | 1 | dx.doi.org/10.17504/protocols.io.5qpvor38xv4o/v1 | https://www.protocols.io/view/intelligent-job-and-career-recommender-systems-a-s-cjeyujfw | Maximin Lange, Ricardo Twumasi, nikos koutsouleris | TITLE: Intelligent Job and Career Recommender Systems: A Systematic Review
AUTHORS: Maximin Lange, Ricardo Twumasi, nikos koutsouleris
[DESCRIPTION]
We are supplying the first systematic review on intelligent job recommender systems (IJRS). In this work, we analyse prominent issues and problems regarding IJRSand remed... | ["[Methodology] Methodology\nAs Suddaby et al. (2017) note, when systematically reviewing existing research, several methods are available to the researcher, which have been distinguished by Noblit and Hare (1988) as either integrative or interpretive. While integrative reviews are to be chosen when analysed material i... |
32,045 | Participant Recruitment and Enrollment | null | dx.doi.org/10.17504/protocols.io.bbimikc6 | null | Alyssa Ward, Gracie Gordon, Jimmie Ye | TITLE: Participant Recruitment and Enrollment
AUTHORS: Alyssa Ward, Gracie Gordon, Jimmie Ye
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The Immune Cell Census aims to collect expression data from 1000 blood samples collected from healthy individuals. This protocol outlines our inclusion/exclusi... | ["[Participant Recruitment]\nOur study team maintains fliers that direct participants to the immunecensus.org website and give our study email address (immunecensus@ucsf.edu). After participants express interest, we schedule a phone screen.", "[Phone Screen]\nEnsure participants understand that the de-identified (no na... |
69,801 | Antioxidant rescue of C. elegans behaviour on Keio E. coli mutants (6-well plates) | 1 | dx.doi.org/10.17504/protocols.io.j8nlkw5kdl5r/v1 | https://www.protocols.io/view/antioxidant-rescue-of-c-elegans-behaviour-on-keio-cgehttb6 | Saul Moore | TITLE: Antioxidant rescue of C. elegans behaviour on Keio E. coli mutants (6-well plates)
AUTHORS: Saul Moore
[DESCRIPTION]
Protocol for screening candidate behaviour-modifying E. coli BW25113 single-gene deletion mutants from the 'Keio Collection', to investigate their effects on Caenorhabditis elegans behaviour in... | ["[Preparing NGM agar + pouring plates] Prior to screening, prepare the materials needed for screening C. elegans on selected Keio E. coli mutants:\n\n- 6-well plates (aka. 'imaging plates')\n- 15 mL Falcon tubes\n- 50 mL Erlenmeyer flasks\n- 90 mm Petri plates (aka. 'maintenance plates')\n- 150 mm Petri plates (aka. '... |
23,032 | Observational, Real World Study of Osimertinib for Patients with Locally advanced/Metastatic T790M Mutation-Positive An observational, retrospective study conducted among locally advanced or metastatic T790M mutation-positive NSCLC patients progressed afte | null | dx.doi.org/10.17504/protocols.io.2qygdxw | null | Yabing Cao | TITLE: Observational, Real World Study of Osimertinib for Patients with Locally advanced/Metastatic T790M Mutation-Positive An observational, retrospective study conducted among locally advanced or metastatic T790M mutation-positive NSCLC patients progressed afte
AUTHORS: Yabing Cao
[DESCRIPTION]
<div class = "text-bl... | ["Study Timetable and Early Termination of Enrolment and StudyThe end of the study is defined as ‘the last visit of the last patient undergoing the study’. Thestudy is expected to start in Quarter 1 2017 and to end by Quarter 3 2017AstraZeneca reserves the right to terminate the enrolment of the study. Should AstraZene... |
92,995 | Protocol for eDNA extraction within STERIVEX capsule based on Spens et al. 2017 | 1 | dx.doi.org/10.17504/protocols.io.eq2lyj58rlx9/v1 | https://www.protocols.io/view/protocol-for-edna-extraction-within-sterivex-capsu-c63bzgin | delphine.vanhaecke | TITLE: Protocol for eDNA extraction within STERIVEX capsule based on Spens et al. 2017
AUTHORS: delphine.vanhaecke
[DESCRIPTION]
This protocol for eDNA extraction from STERIVEX filters within the capsule is modified from the protocol published by Spens et al. 2017. (DOI:10.1111/2041-210X.12683) based on the DNeasy‱ bl... | ["[DAY 1] Clean the laminar flow hood and micropipettes with DNAZAP, wipe with ddH2O and 70% Ethanol using tissue paper.", "[DAY 1] Place gloves, sleeves, 1.5 mL (8) and 2.0 ml (24) sterilized LoBind tubes in the laminar flow hood and expose for 10min to UV light. (1.5 mL tubes for receiving eDNA eluate, 2.0 mL tubes f... |
39,572 | Phenol-based RNA extraction from polycarbonate filters | 4 | dx.doi.org/10.17504/protocols.io.bivuke6w | https://www.protocols.io/view/phenol-based-rna-extraction-from-polycarbonate-fil-bivuke6w | Robbie M. Martin, Steven W. Wilhelm | TITLE: Phenol-based RNA extraction from polycarbonate filters
AUTHORS: Robbie M. Martin, Steven W. Wilhelm
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is an acid-phenol-based method for extracting RNA from samples collected onto polycarbonate filters. Bead-beating is included to i... | ["[Phenol-based RNA Extraction]\nAdd 700 µL of Solution A (lysing buffer) to an MP Biomedical Lysing Matrix E tube (or equivalent bead beating tube). Solution A consists of 0.5% SDS, 20 mM sodium acetate, and 10 mM EDTA in RNase-free molecular biology grade water.", "[Phenol-based RNA Extraction]\nPre-chill tube cont... |
null | null | null | dx.doi.org/10.17504/protocols.io.hwhb7b6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes a method for detecting T cell activation in response to BiTE<strong>®</strong> treatment by flow cytometry .</p>
[STEPS]
?.
?.
?.
?. | [] |
40,703 | ELISA for quantification of IL-6 in human serum or plasma. | 6 | dx.doi.org/10.17504/protocols.io.bjy7kpzn | https://www.protocols.io/view/elisa-for-quantification-of-il-6-in-human-serum-or-bjy7kpzn | Angel Justiz-Vaillant | TITLE: ELISA for quantification of IL-6 in human serum or plasma.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Interleukin-10 is a pleiotropic cytokine playing a critical role as a regulator of myeloid and lymphoid cell function. Due to the ability of IL-10 to bloc... | ["An anti-human IL-6 coating antibody is adsorbed onto microwells by incubation overnight at 4°C.", "Add 50 µl of human serum. Human IL-6 present in the serum sample binds to antibodies adsorbed to the microwells.", "The microplate is blocked with 3% non-fat milk-PBS buffer and later wasth o remove unbound proteins.",... |
null | null | null | dx.doi.org/10.17504/protocols.io.mwqc7dw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The aim of this study was to systematically review and analyze the published preclinical studies of MSC administration in the treatment of animal models of PQ poisoning to provide a basis for cell therapy of PQ poisoning.The electronic databases PubMed and CBMdisc were search... | [] |
26,028 | A multi-scale model of cardiac electrophysiology | null | dx.doi.org/10.17504/protocols.io.5nkg5cw | null | Colleen clancy, Pei-Chi, Parya Aghasafari | TITLE: A multi-scale model of cardiac electrophysiology
AUTHORS: Colleen clancy, Pei-Chi, Parya Aghasafari
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Multi-scale computational modeling is a major branch of computational biology as evidenced by the US federal interagency Multi-Scale Modeling Con... | ["Creating multi-scale model of cardiac electrophysiologyWe developed a workflow containing differential equation models of cardiac physiology that automate the execution of simulations with user defined options of outputs from a single cell, 1 or 2D tissue, and a pseudo-ECG output, which can be compared to experimenta... |
57,858 | Introductory Hydra Activities | 1 | dx.doi.org/10.17504/protocols.io.b4raqv2e | https://www.protocols.io/view/introductory-hydra-activities-b4raqv2e | Callen Hyland | TITLE: Introductory Hydra Activities
AUTHORS: Callen Hyland
[DESCRIPTION]
This is a series of introductory lab activities for BIOL309-03: Research Methods. The purpose is to master vocabulary related to Hydra anatomy, become familiar with compound microscopes and dissecting microscopes, and practice microdissections ... | ["[Observation Activities] In this activity you will become familiar with the anatomy of Hydra including areas of the body, cell layers, and nematocysts, while practicing the new vocabulary we learned in lecture.\n\nLearning objectives:\nUse a compound microscope to examine prepared slides\nMaster vocabulary related to... |
62,742 | Protein extraction, quantification, and western blot for Bodo saltans | 4 | dx.doi.org/10.17504/protocols.io.5qpvobqodl4o/v2 | https://www.protocols.io/view/protein-extraction-quantification-and-western-blot-b9hwr37e | Ewa Chrostek, Mastaneh Ahrar, Gregory Dd Hurst | TITLE: Protein extraction, quantification, and western blot for Bodo saltans
AUTHORS: Ewa Chrostek, Mastaneh Ahrar, Gregory Dd Hurst
[DESCRIPTION]
This protocol is used in our Laboratory in Liverpool to work with proteins from Bodo saltans and other kinetoplastids (eg. trypanosomes).
[STEPS]
SECTION: Culture co... | ["[Culture conditions] Bodo saltans was cultured in a cerophyl-based medium enriched with 3.5 mM sodium phosphate dibasic (Na2HPO4)1. Cultures were incubated at 22 °C in T25 tissue culture flasks containing 20 ml of media bacterized with Klebsiella pneumoniae subsp. Pneumoniae (ATCC® 700831).", "[Protein extraction and... |
24,487 | Ethanol precipitation of RNA from small or large volumes | null | dx.doi.org/10.17504/protocols.io.36fgrbn | null | Stephen Floor | TITLE: Ethanol precipitation of RNA from small or large volumes
AUTHORS: Stephen Floor
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">How to precipitate RNA with ethanol and resuspend it! Two separate protocols - one for small and one for large volumes. The procedure for large volume precipitation ... | ["[Precipitating RNA (< 500 ul sample volume)]\nAdd 1 ul glycoblue per 250 ul sample volume\nvolume here is the volume after adding NaOAc, not the original volume.", "[Precipitating RNA (< 500 ul sample volume)]\nVortex briefly", "[Precipitating RNA (< 500 ul sample volume)]\nAdd 2 volumes 100% ethanol\nvolume here is ... |
28,166 | Neuropathy Phentoyping Protocols - Intra-Epidermal Fiber Density Determination of Rodent Foot Pad Biopsies | null | dx.doi.org/10.17504/protocols.io.7rehm3e | null | Eva Feldman | TITLE: Neuropathy Phentoyping Protocols - Intra-Epidermal Fiber Density Determination of Rodent Foot Pad Biopsies
AUTHORS: Eva Feldman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block"><span style = "font-weight:bold;">Ph... | ["Perfused mouse or rat: 1. Following perfusion, remove entire foot pad with a sharp razor blade. Begin by cutting skin between the plantar surface of the foot and the toes, then start at the heel to gently remove the skin and superficial fascia of the foot. Be careful to only handle the tissue by the heel. 2. Post-fix... |
87,489 | Uncovering the Citation Landscape: Exploring OpenCitations COCI, OpenCitations Meta, and ERIH-PLUS in Social Sciences and Humanities Journals - Workflow | 5 | dx.doi.org/10.17504/protocols.io.n92ldpeenl5b/v4 | https://www.protocols.io/view/uncovering-the-citation-landscape-exploring-openci-czn9x5h6 | Marta Soricetti, Sara Vellone, Olga Pagnotta, Lorenzo Paolini | TITLE: Uncovering the Citation Landscape: Exploring OpenCitations COCI, OpenCitations Meta, and ERIH-PLUS in Social Sciences and Humanities Journals - Workflow
AUTHORS: Marta Soricetti, Sara Vellone, Olga Pagnotta, Lorenzo Paolini
[DESCRIPTION]
Purpose
The main purpose of this research is to answer to three different... | ["[Processing of Input Data] We tried to define a mapping of the datasets to understand what are the information that the three datasets have in common. By looking at the data and the columns' names, we have identified the following:\n \nTaking as a starting point META, we have identified the COCI columns \"citing\" an... |
85,710 | Sanger Tree of Life RNA Extraction: Automated MagMax™ mirVana | 4 | dx.doi.org/10.17504/protocols.io.6qpvr36n3vmk/v1 | https://www.protocols.io/view/sanger-tree-of-life-rna-extraction-automated-magma-cxxnxpme | Raquel Juliana Vionette do Amaral, Adam AB Bates, Amy Denton, Halyna Yatsenko, Jessie Jay, Caroline Howard | TITLE: Sanger Tree of Life RNA Extraction: Automated MagMax™ mirVana
AUTHORS: Raquel Juliana Vionette do Amaral, Adam AB Bates, Amy Denton, Halyna Yatsenko, Jessie Jay, Caroline Howard
[DESCRIPTION]
This protocol describes the automated extraction of RNA from multiple different tissue samples intended for RNA-Seq usin... | ["[Reagent Preparation] Prepare the TURBO DNase solution as described below, and once made, store on wet ice: \n ComponentVolume per sample (µL)MagMAX TURBO DNase Buffer60Turbo DNase (stored in freezer)2.5", "[Reagent Preparation] Prepare the Binding Beads Mix as described below, and once made, store on wet ice: \n C... |
37,567 | Lying and Shirking Under Oath | 1 | dx.doi.org/10.17504/protocols.io.bgw7jxhn | https://www.protocols.io/view/lying-and-shirking-under-oath-bgw7jxhn | Nicolas Jacquemet, Stéphane Luchini, Alexander James [Department of Economics, James J Murphy, Jason F Shogren | TITLE: Lying and Shirking Under Oath
AUTHORS: Nicolas Jacquemet, Stéphane Luchini, Alexander James [Department of Economics, James J Murphy, Jason F Shogren
[STEPS] | [] |
73,258 | Whole genome amplification of dengue virus type 1 - 4 | 4 | dx.doi.org/10.17504/protocols.io.6qpvr486pgmk/v1 | https://www.protocols.io/view/whole-genome-amplification-of-dengue-virus-type-1-cjsiunce | Anna Nagy | TITLE: Whole genome amplification of dengue virus type 1 - 4
AUTHORS: Anna Nagy
[DESCRIPTION]
Dengue virus is one of the most often imported tropical viral infection in Hungary. For next-generation whole genome sequencing of dengue virus serotypes 1 - 4, a one-step reverse transcription PCR assay was developed. PCR am... | ["Nucleic acid extraction: \nUse Qiagen QIAamp Viral RNA Mini Kit (cat. no. 52904 or 52906) for nucleic acid extraction. Nucleic acid extraction should be done by following the manufacturer's instructions. The total volume of the extracted viral RNA is 60 µl.", "One-Step Reverse transcription (RT) PCR Setup", "Reagent ... |
33,939 | High Efficiency Transformation Protocol (C2987H) | 1 | dx.doi.org/10.17504/protocols.io.bddti26n | https://www.protocols.io/view/high-efficiency-transformation-protocol-c2987h-bddti26n | New England Biolabs | TITLE: High Efficiency Transformation Protocol (C2987H)
AUTHORS: New England Biolabs
[DESCRIPTION]
This is the protocol for C2987H cells. If you are using the C2987I cells, please refer to this protocol.
[BEFORE_START]
For this protocol, perform steps 1-8 in the tube provided.
[GUIDELINES]
Transformation Protoco... | ["Thaw a tube of NEB 5-alpha Competent E. coli cells on ice for 10 min.", "Add 1 µL-5 µL containing 1 pg-100 ng to the cell mixture.", "Carefully flick the tube 4-5 times to mix cells and DNA. Do not vortex.", "Place the mixture on ice for 30 min. Do not mix.", "Heat shock at exactly 42 °C for exactly 30 s. Do not mix.... |
null | null | null | dx.doi.org/10.17504/protocols.io.guqbwvw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is a guide to using IRDye Subclass Specific antibodies for In-Cell Western™ Assay (ICW) applications. For more detailed descriptions of ICW techniques, refer to Western Blot Analysis and In-Cell Western Kits I and II on the LI-COR Biosciences website (<a href="h... | ["{\"blocks\":[{\"key\":\"e36po\",\"text\":\"Using a multi-channel pipettor, block cells by adding 150 \\u03bcL of Odyssey\\u00ae Blocking Buffer to each well.\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]},{\"key\":\"ainbi\",\"text\":\" \",\"type\":\"atomic\",\"depth\":0,... |
75,144 | Quantification of pollen cysteine contents by PITC derivatization | 6 | dx.doi.org/10.17504/protocols.io.kqdg3983eg25/v1 | https://www.protocols.io/view/quantification-of-pollen-cysteine-contents-by-pitc-cmmgu43w | Mark J. Carroll | TITLE: Quantification of pollen cysteine contents by PITC derivatization
AUTHORS: Mark J. Carroll
[DESCRIPTION]
This protocol quantifies cysteine residues from small amounts of pollen (10 mg) after phenylisothiocyanate (PITC) derivatization (adapted from Manneberg et al 1995). Quantification of cysteine by other meth... | ["[Acid Hydrolysis and Oxidation of Pollen Samples] Create a cysteine external standard in water. Free cysteine is nearly insoluble in water and should be prepared at dilute concentrations. Make a 1 µg cysteine/mL ethanolic water stock solution. Start by dissolving cysteine in ethanol at 10x final concentration, then d... |
40,079 | Trypsin digestion | 3 | dx.doi.org/10.17504/protocols.io.bjdpki5n | https://www.protocols.io/view/trypsin-digestion-bjdpki5n | avinash.kale | TITLE: Trypsin digestion
AUTHORS: avinash.kale
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.nnddda6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>To isolate epithelial cells for sorting from the mouse small intestine </p>
[BEFORE_START]
<p>Put PBS into fridge for use. Only use cold PBS. </p>
[GUIDELINES]
<p>Work quickly and on ice. Keep PBS on ice throughout protocol to maintain cold. Keep extra PBS at +4.</p>
[STEP... | [] |
102,463 | Immunofluorescence staining on larval and adult Drosophila gonads | 0 | dx.doi.org/10.17504/protocols.io.n2bvjnd7ngk5/v1 | https://www.protocols.io/view/immunofluorescence-staining-on-larval-and-adult-dr-dga73shn | Samantha Goetting | TITLE: Immunofluorescence staining on larval and adult Drosophila gonads
AUTHORS: Samantha Goetting
[DESCRIPTION]
Immunofluorescence staining protocol for Drosophila gonads
[BEFORE_START]
All steps are done with gentle rotation.
[STEPS]
SECTION: Day 1
1. Dissect tissue in 1x PBS. Transfer to a 1.5 mL tube containing... | ["[Day 1] Dissect tissue in 1x PBS. Transfer to a 1.5 mL tube containing 1x PBS. If it is a quick dissection (<20 mins), no ice needed. If more time is needed, keep samples on ice.", "[Day 1] Remove PBS and add fixative. Fix in 4% paraformaldehyde in 0.3% PBTx for 20 min RT with gentle rotation. \n 500 uL fixati... |
84,191 | Nanodrop Lite (Shared Equipment Lab) | 4 | null | https://www.protocols.click/view/nanodrop-lite-shared-equipment-lab-cwf7xbrn | Nimalka M Weerasuriya | TITLE: Nanodrop Lite (Shared Equipment Lab)
AUTHORS: Nimalka M Weerasuriya
[DESCRIPTION]
How to use the Nanodrop Lite.
[BEFORE_START]
It is best to use a precision pipettor (0-2 μl) with precision tips to ensure that sufficient sample (1-2 μl) is delivered. Lower precision pipettors (0-10 μl and larger) are not as go... | ["[Setup] Open arm or push any button to wake instrument.\nUsing the bottle of deionized water, slightly wet a Kimwipe and clean the lower and upper pedestal (metal prongs).", "[Nucleic Acid Measurements] Select the appropriate application from the Home screen (DNA or RNA). For DNA measurements, select either the dsDNA... |
87,378 | Sanger Tree of Life HMW DNA Extraction: Manual Plant MagAttract v.4 | 4 | dx.doi.org/10.17504/protocols.io.261ged5k7v47/v1 | https://www.protocols.io/view/sanger-tree-of-life-hmw-dna-extraction-manual-plan-czjsx4ne | Benjamin Jackson, Caroline Howard | TITLE: Sanger Tree of Life HMW DNA Extraction: Manual Plant MagAttract v.4
AUTHORS: Benjamin Jackson, Caroline Howard
[DESCRIPTION]
This protocol describes the manual extraction of HMW DNA from plant or fungi tissue samples from a variety of species intended for long-read sequencing, using the Qiagen MagAttract HMW DN... | ["[Sample lysis] Prepare a lysis buffer master mix in a 50 mL centrifuge tube:\n ReagentVolume per samplePhosphate buffered solution (PBS)200 µLBuffer AL150 µL", "[Sample lysis] Place the lysis buffer on the 65 °C heat block and incubate at 400 rpm for at least 20 minutes. Keep at temperature until added to the sample... |
33,203 | Acid nucleic extraction from rice dried leaves | null | dx.doi.org/10.17504/protocols.io.bcntiven | https://www.protocols.io/view/acid-nucleic-extraction-from-rice-dried-leaves-bcntiven | Martine Bangratz, Charlotte Tollenaere | TITLE: Acid nucleic extraction from rice dried leaves
AUTHORS: Martine Bangratz, Charlotte Tollenaere
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Acid nucleic extraction of rice dried leaves by a CTAB method adapted from Li et al 2008.</div><div class = "text-block"> Li R, Mock R, Huang Q, Abad... | ["Grind the dried leaves with the Qiagen TissueLyser II until obtaining a fine powder", "Add 1 ml CTAB extraction buffer (see 'before start' for the buffer content) and homogenize by vortexing.", "Incubate at 65°C for 30 min. Periodically, mix gently the tubes during the incubation.\n65 °C\nCentrifuge: 10000 34, 10 mi... |
35,897 | NEBExpress Ni-NTA Magnetic Beads (NEB #S1423) | null | null | https://www.protocols.io/view/nebexpress-ni-nta-magnetic-beads-neb-s1423-bfazjif6 | New England Biolabs | TITLE: NEBExpress Ni-NTA Magnetic Beads (NEB #S1423)
AUTHORS: New England Biolabs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-style:italic;">NEBExpress</span><span style = "font-style:italic;vertical-align:super;">®</span><span style = "font-style:italic;">Ni-NTA Magnetic Be... | ["[Buffer Preparation for NEBExpress Ni-NTA Magnetic Beads]\nPrepare the following buffers: ABCD1Lysis/Binding Buffer:\n20 mM sodium phosphate,\n300 mM NaCl,\n10 mM ImidazoleWash Buffer:\n20 mM sodium phosphate,\n300 mM NaCl,\n20 mM ImidazoleElution Buffer:\n20 mM sodium phosphate,\n300 mM NaCl,\n500 mM Imidazole22X I... |
null | null | null | dx.doi.org/10.17504/protocols.io.ibucanw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The protocol decribes the procedure and results of our attempts to transform several species of marine protists by nucleofection.</p>
[STEPS]
?.
?.
?. | [] |
40,696 | Enzyme linked immunosorbent assay (ELISA) for determining the serum concentration of IL-17 in humans. | 4 | dx.doi.org/10.17504/protocols.io.bjyykpxw | https://www.protocols.io/view/enzyme-linked-immunosorbent-assay-elisa-for-determ-bjyykpxw | Angel Justiz-Vaillant | TITLE: Enzyme linked immunosorbent assay (ELISA) for determining the serum concentration of IL-17 in humans.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Interleukin17A is a pro-inflammatory cytokine. This protein is produced by a group of T helper cell known as T-... | ["Ninety-six well ELISA plates are coated with monoclonal anti-human antibodies to interleukin-17( IL-17).", "Patient serum samples are added to the plates.", "The plate is incubate x 1.30 hour at RT.", "The plate is washed 4 times with PBS-tween 20 buffer.", "The wells are incubated with a biotin conjugated anti-human... |
38,959 | Huh7.5_SOP | 4 | dx.doi.org/10.17504/protocols.io.biapkadn | https://www.protocols.io/view/huh7-5-sop-biapkadn | Melissa Teusel, Irina Titkova, Ina Schmitt, Lena Postawa, Marcel Schilling, Ursula Klingmüller | TITLE: Huh7.5_SOP
AUTHORS: Melissa Teusel, Irina Titkova, Ina Schmitt, Lena Postawa, Marcel Schilling, Ursula Klingmüller
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">SOP for thawing, cultivation and freezing of the Huh7.5 cell line by the Division... | ["[Medium]\nGrowth MediumDMEM1% Glutamax10% FCS 1% P/S", "[Thawing of cells]\nPre-warm growth medium in water bath\n37 °C", "[Thawing of cells]\nThaw the cells in a water bath (not completely, there should be a small visible ice clump inside the tube)\n37 °C", "[Thawing of cells]\nTransfer the cells into a 15 ml centr... |
43,867 | Determine the Size of Sonicated Samples and the DNA Concentration | 4 | dx.doi.org/10.17504/protocols.io.bn33mgqn | https://www.protocols.io/view/determine-the-size-of-sonicated-samples-and-the-dn-bn33mgqn | Vasso Makrantoni, Daniel Robertson, Adele L. Marston | TITLE: Determine the Size of Sonicated Samples and the DNA Concentration
AUTHORS: Vasso Makrantoni, Daniel Robertson, Adele L. Marston
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A plethora of biological processes like gene transcription, DNA replication, DNA recombination, and chromosome segreg... | ["[Determine the Size of Sonicated Samples and the DNA Concentration]\nTo a add containing .\n[Input sample]\n[TE buffer]\n[NaCl]", "[Determine the Size of Sonicated Samples and the DNA Concentration]\nDecross-link at .\n65 °C", "[Determine the Size of Sonicated Samples and the DNA Concentration]\nAdd and incubate a... |
40,314 | CUT&Tag Data Processing and Analysis Tutorial | 5 | null | https://www.protocols.io/view/cut-amp-tag-data-processing-and-analysis-tutorial-bjk2kkye | Ye Zheng, Kami Ahmad, Steven Henikoff | TITLE: CUT&Tag Data Processing and Analysis Tutorial
AUTHORS: Ye Zheng, Kami Ahmad, Steven Henikoff
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This tutorial is designed for processing and analyzing CUT&Tag data following the </span><a href="https://www.protocols.io/view/bench-top-cut-amp-... | ["[I. Introduction]\nObjectivesThis tutorial is designed for processing and analyzing CUT&Tag data following the Benchtop CUT&Tag V.3 protocol. The illustration data used in this tutorial is the profiling of histone modifications in the human lymphoma K562 cell line, but the tutorial is generally applicable to any chro... |
51,000 | Mouse kidney cell staining protocol for FACS sorting | 3 | null | https://www.protocols.io/view/mouse-kidney-cell-staining-protocol-for-facs-sorti-bv2yn8fw | Xian Adiconis | TITLE: Mouse kidney cell staining protocol for FACS sorting
AUTHORS: Xian Adiconis
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A brief description on staining and gating for FACS sorting the live cells from dissociated mouse kidney tissue </div></div>
[STEPS] | [] |
82,924 | Enriching and isolating phages on agar plates | 4 | dx.doi.org/10.17504/protocols.io.bp2l69oo1lqe/v1 | https://www.protocols.click/view/enriching-and-isolating-phages-on-agar-plates-cu8kwzuw | Adair Borges | TITLE: Enriching and isolating phages on agar plates
AUTHORS: Adair Borges
[DESCRIPTION]
This protocol explains how we isolate phage from microbial communities on solid agar plates. For a protocol on liquid enrichment and isolation, check out our companion protocol.
[STEPS]
SECTION: Solid-plate phage isolation
1. Set... | ["[Solid-plate phage isolation] Set up cultures of your target host strains. We use this protocol for cheese bacterial isolates, which grow best in LB at 25 °C with shaking at 200 rpm, and reach high density after two days.", "[Solid-plate phage isolation] Prepare your phage extracts to infect your host strains. There ... |
59,003 | Onepot-seq | 4 | null | https://www.protocols.io/view/onepot-seq-b5u3q6yn | Dongju Shin, JungWon Choi, Ji Hyun Lee, Duhee Bang | TITLE: Onepot-seq
AUTHORS: Dongju Shin, JungWon Choi, Ji Hyun Lee, Duhee Bang
[DESCRIPTION]
Onepot-seq protocol follows steps below:
Cells and beads preparation
Scatteration of beads and cells in well
Cell lysis and beads isolation
cDNA synthesis
cDNA Library amplification
NGS preparation
[GUIDELINES]
Onepot-seq i... | ["[Cells and beads preparation] Suspend cells in PBS (1,000 cells/μl of concentration is recommended)", "[Cells and beads preparation] Suspend beads in incubation buffer (20,000 beads in 100 µL incubation buffer)\n(incubation buffer : 6% Ficoll PM-400, 20mM EDTA, 0.2M Tris pH 7.5)", "[Scatteration of beads and cells in... |
13,208 | Single-strand library preparation protocol | 1 | dx.doi.org/10.17504/protocols.io.q5ydy7w | https://www.protocols.io/view/single-strand-library-preparation-protocol-q5ydy7w | Tomasz Suchan | TITLE: Single-strand library preparation protocol
AUTHORS: Tomasz Suchan
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [ Guanidine tailing]
Prepare master mix 2 (assemble at room temperature, can precipitate when on ice):
[water]
[NEBuffer 4 (10x)]
[CoCl2 (2.5 mM)]
[GTP (100 mM)]
[TdT (20 U/μl)]
?. [Seco... | ["[ Guanidine tailing]\nPrepare master mix 2 (assemble at room temperature, can precipitate when on ice):\n[water]\n[NEBuffer 4 (10x)]\n[CoCl2 (2.5 mM)]\n[GTP (100 mM)]\n[TdT (20 U/μl)]", "[Second strand synthesis]\nPrepare master mix 3:\n[water]\n[NEBuffer 4 (10x)]\n[dNTP mix (25 mM each)]\n[P2-CCCCC oligo (15 mM)]\n[... |
25,672 | Attachment 1: Preparation of Fluorescein Diacetate and Propidium Iodide Stock Solutions (FDA/PI) | null | dx.doi.org/10.17504/protocols.io.5bgg2jw | null | Integrated Islet Distribution Program, Carol J Swanson, Barbara Olack | TITLE: Attachment 1: Preparation of Fluorescein Diacetate and Propidium Iodide Stock Solutions (FDA/PI)
AUTHORS: Integrated Islet Distribution Program, Carol J Swanson, Barbara Olack
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This Standard Operating Procedure is adapted from the work of ... | ["[Preparation of Stock Fluorescein Diacetate (FDA) Solution]\nPrepare Fluorescein Diacetate (FDA) according to the formulation in sub-steps below.\nThe expiration date, for both PI and FDA stains, is six months from the date of preparation. Both of the fluorescent dyes used in this assay are light sensitive and must ... |
81,586 | Differentiation of human medium spiny neurons (MSNs) from induced pluripotent stem cells (iPSCs) | 4 | dx.doi.org/10.17504/protocols.io.eq2ly79prlx9/v1 | https://www.protocols.io/view/differentiation-of-human-medium-spiny-neurons-msns-ctwswpee | Quyen Do, Nora Bengoa-Vergniory, Richard Wade-Martins | TITLE: Differentiation of human medium spiny neurons (MSNs) from induced pluripotent stem cells (iPSCs)
AUTHORS: Quyen Do, Nora Bengoa-Vergniory, Richard Wade-Martins
[DESCRIPTION]
This protocol generates human medium spiny neurons (MSNs) from induced human pluripotent stem cells. Incorporating key findings from Telz... | ["[Differentiation of iPSCs into Neuronal Progenitor Cells (NPCs)] Day -2: Preparing plates for replating\nTwo days before intending on starting the differentiation (Day -2), add 1 mL/well in a 6-well plate of Geltrex one day prior to replating the iPSCs to begin the differentiation.", "[Differentiation of iPSCs into N... |
39,227 | High-Yield Skeletal Muscle Protein Recovery from TRIzol® after RNA and DNA Extraction | 6 | dx.doi.org/10.17504/protocols.io.bii3kcgn | https://www.protocols.io/view/high-yield-skeletal-muscle-protein-recovery-from-t-bii3kcgn | Yuan Wen, Ivan Vechetti , Taylor Valentino, John J McCarthy | TITLE: High-Yield Skeletal Muscle Protein Recovery from TRIzol® after RNA and DNA Extraction
AUTHORS: Yuan Wen, Ivan Vechetti , Taylor Valentino, John J McCarthy
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Extraction of DNA, RNA, and protein from the same sample would allow for direct comparison... | ["[RNA Extraction]\nMince muscle tissue into small (~10 mg) pieces.", "[RNA Extraction]\nIsolate RNA using TRIzol® reagent, following manufacturer’s instructions.Important point: Use 0.5 ml of TRIzol® reagent per piece (Important point: For better phase separation, use 100 µl of BCP instead of Chloroform.", "[RNA Extra... |
37,461 | Non-radioactive phosphorylation with T4 PNK 3' phosphatase minus (M0236) | 1 | dx.doi.org/10.17504/protocols.io.4rm7vzdrlx1w/v2 | https://www.protocols.io/view/non-radioactive-phosphorylation-with-t4-pnk-3-39-p-bgtvjwn6 | New England Biolabs | TITLE: Non-radioactive phosphorylation with T4 PNK 3' phosphatase minus (M0236)
AUTHORS: New England Biolabs
[DESCRIPTION]
Protocol for non-radioactive phosphorylation with T4 PNK 3' phosphatase minus.
[STEPS]
1. Set up the following reaction in a microcentrifuge tube on ice:
2. Incubate at 37 °C for 30... | ["Set up the following reaction in a microcentrifuge tube on ice:", "Incubate at 37 °C for 30 min.", "Heat inactivate by incubating at 65 °C for 20 min."] |
26,444 | Measure feeding during large population swarming with bioluminescent bacteria | null | dx.doi.org/10.17504/protocols.io.53kg8kw | null | Serena Ding | TITLE: Measure feeding during large population swarming with bioluminescent bacteria
AUTHORS: Serena Ding
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Protocol uses bioluminescently labelled bacteria (Gregor et al, 2008, Addgene Plasmid #107879, </span><a href="https://www.pnas.org/content/... | ["[Grow bacteria overnight]\nDay -2 Streak out bioluminescent bacteria frozen stock onto an LB plate containing 50 μg/mL ampicillin and incubate overnight at .\n37 °C\nThis step does not need to be performed every time. A streaked plate can be re-used within 1 month, so long as single colonies are still available. Othe... |
55,790 | Nuclei Isolation with EZ Prep Kit | 1 | dx.doi.org/10.17504/protocols.io.36wgq7r8yvk5/v1 | https://www.protocols.io/view/nuclei-isolation-with-ez-prep-kit-b2qnqdve | Le Zhang | TITLE: Nuclei Isolation with EZ Prep Kit
AUTHORS: Le Zhang
[DESCRIPTION]
This protocol details nuclei Isolation with EZ Prep Kit.
[STEPS]
1. Prepare nuclei suspension buffer by adding2 µLof RNase Inhibitor (40 U/μl) per mL of nuclei suspension buffer. Vortex briefly to mix.
2. Keeping everything on ice, add 1 mL E... | ["Prepare nuclei suspension buffer by adding2 µLof RNase Inhibitor (40 U/μl) per mL of nuclei suspension buffer. Vortex briefly to mix.", "Keeping everything on ice, add 1 mL EZ PREP buffer (Sigma, NUC101) and tissue piece to the small 2 mL glass tissue grinder. Grind 3 times just to mash the tissue at the bottom of ... |
null | null | null | dx.doi.org/10.17504/protocols.io.pufdntn | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p>This protocol is used to assess the sgRNA-to-barcode linkage in Mosaic-seq. The 3kb fragment can be amplified from either plasmids or genomic DNA extract from cells after lentivirual infection. The fragments are then circularized and used to amplify a smaller amplicon (about 2... | [] |
81,561 | iPhone LiDAR tutorial | 1 | dx.doi.org/10.17504/protocols.io.yxmvm21w9g3p/v2 | https://www.protocols.io/view/iphone-lidar-tutorial-ctvzwn76 | Gregor Luetzenburg | TITLE: iPhone LiDAR tutorial
AUTHORS: Gregor Luetzenburg
[DESCRIPTION]
Recording, exporting and analyzing iPhone LiDAR data
The aim of this tutorial is to provide a guide on how to create models of the earth surface on a small to medium scale with the LiDAR sensor built in the Apple iPhones, edit and export those mo... | ["[Recording data] 3d Scanner App basic functionality\n\nTo record data with the iPhone LiDAR scanner, unlock the iPhone and open the 3d Scanner App. Make sure nothing obstructs the LiDAR scanner at the back of the iPhone. By default, the app opens the ‘camera interface’ which is used for scanning 3D models. While scan... |
75,641 | CUMC-TMC-10X-Gene-Expression | 1 | null | https://www.protocols.io/view/cumc-tmc-10x-gene-expression-cm4zu8x6 | Shaunice Grier | TITLE: CUMC-TMC-10X-Gene-Expression
AUTHORS: Shaunice Grier
[DESCRIPTION]
Post Mortem Human Fresh Frozen Dorsolateral Prefrontal Cortex tissues are cryo - sectioned onto 10X Visium slides.
Tissue Optimization is performed and determines optimal Gene Expression testing conditions.
cDNA samples are processed and gener... | ["[Tissue QC] Section", "[Tissue QC] H&E Stain", "[Tissue QC] Image", "[Tissue QC] Assess", "[Tissue Optimization] Permeabilization & cDNA Synthesis", "[Tissue Optimization] Tissue Removal", "[Gene Expression] cDNA Synthesis", "[Gene Expression] Second Strand Synthesis & Denaturation", "[Gene Expression] cDNA Amplifica... |
null | null | null | dx.doi.org/10.17504/protocols.io.qn9dvh6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><span style="font-weight: 400;">Mu-DNA is designed to be a simple and modular spin column-based DNA extraction ‘toolkit’ for the isolation of high purity DNA from multiple sample types. Here we present optimised Mu-DNA protocols for soil, tissue and water samples. Each protoc... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.qz8dx9w | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
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44,240 | Automated Chloroform-Methanol Protein Extraction on the Biomek-FX Liquid Handler System | 4 | dx.doi.org/10.17504/protocols.io.bpfqmjmw | https://www.protocols.io/view/automated-chloroform-methanol-protein-extraction-o-bpfqmjmw | Yan Chen, Tad Ogorzalek, Nurgul Kaplan Lease, Jennifer Gin, Christopher J Petzold | TITLE: Automated Chloroform-Methanol Protein Extraction on the Biomek-FX Liquid Handler System
AUTHORS: Yan Chen, Tad Ogorzalek, Nurgul Kaplan Lease, Jennifer Gin, Christopher J Petzold
[DESCRIPTION]
This protocol details steps to extract protein from Gram-negative bacterial or fungal cells (that have been pretrea... | ["[Protein Extraction] Transfer 87.5 µl water from water reservoir to cell plate. Mix and resuspend cell pellet on deck with user defined times.", "[Protein Extraction] The PAUSE step prompts you to centrifuge your plate.", "[Protein Extraction] Centrifuge 2000 x g, 2 min, 25 °C .", "[Protein Extraction] Put plate bac... |
54,381 | in vivo cloning (iVEC) | 1 | null | https://www.protocols.io/view/in-vivo-cloning-ivec-bzcmp2u6 | Yuichiroh Ikagawa | TITLE: in vivo cloning (iVEC)
AUTHORS: Yuichiroh Ikagawa
[DESCRIPTION]
In vivo cloning is a seamless cloning method in which a DNA fragment, to which a homologous sequence has been added by PCR, is introduced directly into Escherichia coli SN1187 for assembly and cloning in the bacterium. The 5' end of the DNA fragme... | ["[Transformation] Add 100 ng of DNA samples (vector and insert) into the competent cell.", "[Transformation] Mix by gently pipetting and incubate for 20 minutes on ice.", "[Transformation] Add 1 ml SOC medium and mix by carefully inverting", "[Transformation] Incubate at 37℃ for 1 hour.", "[Transformation] Centrifuge ... |
44,507 | WASP-D Field Protocol | 4 | null | https://www.protocols.io/view/wasp-d-field-protocol-bpp3mmqn | Greg Blonder | TITLE: WASP-D Field Protocol
AUTHORS: Greg Blonder
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>WASP-D (</span><span style = "font-weight:bold;">W</span><span>arm</span><span style = "font-weight:bold;">A</span><span>nd</span><span style = "font-weight:bold;">S</span><span>low</span><span s... | ["Before used-PPE is submitted for decontamination, the user should indelibly mark their PPE with their name and current date. Since WASP-D cannot guarantee all possible pathogens are fully deactivated, an “index” method where PPE is returned to the original user is prudent, though not required. Used-PPE often takes th... |
48,542 | Citric acid nuclei isolation from frozen oesophageal tissue | 4 | dx.doi.org/10.17504/protocols.io.btm6nk9e | https://www.protocols.io/view/citric-acid-nuclei-isolation-from-frozen-oesophage-btm6nk9e | Lucy Kimbley, Rachel Parker, Jack Harrington, Robert C. Walker, Ben Grace, Jonathan J. West, Tim J. Underwood, Matthew Rose Zerilli | TITLE: Citric acid nuclei isolation from frozen oesophageal tissue
AUTHORS: Lucy Kimbley, Rachel Parker, Jack Harrington, Robert C. Walker, Ben Grace, Jonathan J. West, Tim J. Underwood, Matthew Rose Zerilli
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Citric acid-based method of isolating nucle... | ["Weigh tissue. 30-40mg of tissue should be used per experiment. If not using the entire sample, quickly remove the tissue required by chopping sample in a petri dish chilled on dry ice (For RNA Later Ice samples see 1.1) with a cold scalpel. Return unused tissue to LN2.", "If using tissue stored in RNA Later Ice, carr... |
58,068 | Microfluidic Chip Production v1.1 | 1 | dx.doi.org/10.17504/protocols.io.b4xuqxnw | https://www.protocols.io/view/microfluidic-chip-production-v1-1-b4xuqxnw | Florian De Rop, Stein Aerts, Suresh Poovathingal | TITLE: Microfluidic Chip Production v1.1
AUTHORS: Florian De Rop, Stein Aerts, Suresh Poovathingal
[DESCRIPTION]
Protocol for producing microfluidic chips used in HyDrop experiment.
[STEPS]
SECTION: Microfluidic Chip Preparation
1. Producing an SU-8 patterned silicon wafer
Here, we describe how we produce our micr... | ["[Microfluidic Chip Preparation] Producing an SU-8 patterned silicon wafer\nHere, we describe how we produce our microfluidic chips. The most important part is that the x/y dimensions of your droplet generators match ours. The z-dimension (channel height) may vary according to your method of spin-coating and the visco... |
null | null | null | dx.doi.org/10.17504/protocols.io.in7cdhn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Please contact Dr. Steven Wilhelm (wilhelm@utk.edu) for additional information regarding this protocol.</p>
[STEPS]
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27,537 | Single Cell Dissociation of Small Tumor Biopsies | null | dx.doi.org/10.17504/protocols.io.65rhg56 | null | Ashley Maynard | TITLE: Single Cell Dissociation of Small Tumor Biopsies
AUTHORS: Ashley Maynard
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Dissociate small core biopies into single cells.</div></div>
[STEPS]
?. Make and/or warm Base Buffer1 to .
37 °C
?. Pour the sample(s) into a 10cm dish. Take a picture of ... | ["Make and/or warm Base Buffer1 to .\n37 °C", "Pour the sample(s) into a 10cm dish. Take a picture of the samples in a 10cm dish (in the media it comes in).Example:", "Cut sample into small pieces and place into a 1.5mL tube (or multiple tubes if necessary, don’t overload the tube with tissue). Add 1.5 mL of collagenas... |
95,927 | Environmental Impact of Primary Care- Australian Perspective: A Scoping Review | 0 | dx.doi.org/10.17504/protocols.io.14egn35epl5d/v1 | https://www.protocols.io/view/environmental-impact-of-primary-care-australian-pe-c9wxz7fn | jessica.jaja | TITLE: Environmental Impact of Primary Care- Australian Perspective: A Scoping Review
AUTHORS: jessica.jaja
[DESCRIPTION]
Climate Change has significant detrimental impacts on human health, well-being, and mortality. As the first responder during a climate crisis, primary healthcare is implicated by increased patient ... | ["[Background/Purpose] Climate Change has significant detrimental impacts on human health, well-being, and mortality. As the first responder during a climate crisis, primary healthcare is implicated by increased patient demand and burden on the system. Paradoxically, primary healthcare, and the healthcare sector as a w... |
90,588 | Protocol to isolate and fix nuclei from flash frozen male mouse gonads for IGVF | 4 | null | https://www.protocols.io/view/protocol-to-isolate-and-fix-nuclei-from-flash-froz-c4p4yvqw | Elisabeth Rebboah | TITLE: Protocol to isolate and fix nuclei from flash frozen male mouse gonads for IGVF
AUTHORS: Elisabeth Rebboah
[DESCRIPTION]
This protocol describes isolation of nuclei from left and right 10 week old mouse testes and epididymis (pooled tissue ID: 25) from 8 founder strains (B6J, AJ, 129S1J, NZOJ, WSBJ, NODJ, PWKJ,... | ["[Setup] Label tubes.", "[Setup] Pre-chill centrifuge to 4C.", "[Setup] Prepare ice buckets.", "[Setup] Prepare 40 ml lysis buffer in a 50 ml conical tube on ice. Distribute 2.5 ml into 8 gentleMACS C Tubes on ice. Add 200 ul RNase inhibitor to the lysis buffer aliquot the day of the experiment.", "[Setup] Prepare 25 ... |
43,599 | A Bioinformatics Analysis workflow for 16S rRNA Amplicon Sequencing data | 5 | dx.doi.org/10.17504/protocols.io.bntpmemn | https://www.protocols.io/view/a-bioinformatics-analysis-workflow-for-16s-rrna-am-bntpmemn | Lilan Hao | TITLE: A Bioinformatics Analysis workflow for 16S rRNA Amplicon Sequencing data
AUTHORS: Lilan Hao
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Deal with the 16S rRNA amplicon sequencing reads, which sequenced by Ion PGM</span><span style = "vertical-align:super;">TM</span><span> Sequencer... | ["## Convert the bam files to fastq files../bam2fastq-1.1.0/bam2fastq -o vagina/01.trim.data/16_s1.fq ../rawdata/RFEMpxjMAADGAAPGM-47.bam", "## Trim the poly-A/T, multi-N and low-quality sequences.mothur \"#trim.seqs(fasta= vagina/01.trim.data/16_s1.fa, qfile= vagina/01.trim.data/16_s1.qual, minlength=200,maxambig=1,ma... |
76,071 | Planet Microbe Semantic Web Application | 5 | dx.doi.org/10.17504/protocols.io.e6nvwkw19vmk/v2 | https://www.protocols.io/view/planet-microbe-semantic-web-application-cnifvcbn | Kai Blumberg, Alise J Ponsero, Bonnie L Hurwitz | TITLE: Planet Microbe Semantic Web Application
AUTHORS: Kai Blumberg, Alise J Ponsero, Bonnie L Hurwitz
[DESCRIPTION]
Tutorial for the use of the Planet Microbe Semantic Web Application, accompanying the PhD dissertation work of Kai Blumberg.
[STEPS]
SECTION: Home Page
1. Welcome, This is the protocol to accompany th... | ["[Home Page] Welcome, This is the protocol to accompany the use of the Planet Microbe Semantic Web API. This protocol was created as part of Kai Blumberg's PhD dissertation work. This work is contained within this github repository: https://github.com/hurwitzlab/planet-microbe-semantic-web-analysis.\n\nThis protocol i... |
53,710 | RT-qPCR Detection of SARS-CoV-2 from Wastewater Using the AB 7500 | 4 | dx.doi.org/10.17504/protocols.io.bypnpvme | https://www.protocols.io/view/rt-qpcr-detection-of-sars-cov-2-from-wastewater-us-bypnpvme | Jacquelina.Woods , rachel.rodriguez | TITLE: RT-qPCR Detection of SARS-CoV-2 from Wastewater Using the AB 7500
AUTHORS: Jacquelina.Woods , rachel.rodriguez
[DESCRIPTION]
This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in wastewater. Protoco... | ["[Master Mix Preparation] Proceed to hood/area or room where the template is added and thaw IC RNA and sample RNA in this hood/area.", "[Master Mix Preparation] Prepare Master Mix for all sample and control reactions based on the volumes per 25 µl reaction in this table. Composition of mixes are listed here: Reagent M... |
60,559 | Coverage of open citations in DOAJ journals | 1 | dx.doi.org/10.17504/protocols.io.n92ldz598v5b/v1 | https://www.protocols.io/view/coverage-of-open-citations-in-doaj-journals-b7dpri5n | Constance Dami, Alessandro Bertozzi, Chiara Manca, Umut Kucuk | TITLE: Coverage of open citations in DOAJ journals
AUTHORS: Constance Dami, Alessandro Bertozzi, Chiara Manca, Umut Kucuk
[DESCRIPTION]
This is the protocol for the research of the coverage of open citations in DOAJ journals.
Our goal is to find out:
about the coverage of articles from open access journals in DOA... | ["[Data Gathering] First, we create a script for making queries to the OpenCitations API (or SPARQL endpoints).\nWe make the queries on both of the indexes COCI and CROCI.", "[Data Analysis] We do additional analysis of the data that we gathered. Maybe studying the future of the research.", "[Data Visualization] We vis... |
82,711 | Protocols for "Synaptotagmin-1-dependent phasic axonal dopamine release is dispensable for basic motor behaviors in mice" | 2 | dx.doi.org/10.17504/protocols.io.n92ldpoj8l5b/v1 | https://www.protocols.click/view/protocols-for-34-synaptotagmin-1-dependent-phasic-cuzxwx7n | Benoît Delignat-Lavaud, Jana Kano, Charles Ducrot, Ian Massé, Sriparna Mukherjee, Nicolas Giguère, Luc Moquin, Catherine Lévesque, Samuel Burke, Raphaëlle Denis, Marie-Josée Bourque, Alex Tchung, Pedro Rosa-Neto, Daniel Lévesque, Louis De Beaumont, louis-eric.trudeau | TITLE: Protocols for "Synaptotagmin-1-dependent phasic axonal dopamine release is dispensable for basic motor behaviors in mice"
AUTHORS: Benoît Delignat-Lavaud, Jana Kano, Charles Ducrot, Ian Massé, Sriparna Mukherjee, Nicolas Giguère, Luc Moquin, Catherine Lévesque, Samuel Burke, Raphaëlle Denis, Marie-Josée ... | [] |
100,024 | Protocol 2 - MRI data protocol | 5 | dx.doi.org/10.17504/protocols.io.3byl4k8jjvo5/v2 | https://www.protocols.io/view/protocol-2-mri-data-protocol-ddwy27fw | Sophie Adler, Mathilde Ripart, Meld Project, Konrad Wagstyl | TITLE: Protocol 2 - MRI data protocol
AUTHORS: Sophie Adler, Mathilde Ripart, Meld Project, Konrad Wagstyl
[DESCRIPTION]
The MELD Project is an international collaboration aiming to create open-access, robust and generalisable tools for FCD detection.
This MRI data protocol details
1) The MRI data required / desirab... | ["[Retrieval of MRI data] Prepare your data \n\nDownload the meld_focal_epilepsy_data folder from : https://figshare.com/s/763e50f4eb51a4f76f58\n\nKeep note of where you save this folder as it will be your data folder : <path_to_meld_focal_epilepsy_data_folder> \n\nYou will need to unzip the folder :\n\n \n\n\n\nAnonym... |
102,402 | Immunohistochemistry of free floating slices | 0 | dx.doi.org/10.17504/protocols.io.rm7vzj6rrlx1/v1 | https://www.protocols.io/view/immunohistochemistry-of-free-floating-slices-df9a3r2e | louis-eric.trudeau | TITLE: Immunohistochemistry of free floating slices
AUTHORS: louis-eric.trudeau
[DESCRIPTION]
This protocol details the immunohistochemistry of free floating slices.
[STEPS]
SECTION: Steps
1.
Fix with paraformaldehyde (PFA) 4% at Room temperature.
- 4 g of PFA
- Dissolve in 100 mL de PBS (pH pH 7.3) previously ... | ["[Steps] Fix with paraformaldehyde (PFA) 4% at Room temperature.\n- 4 g of PFA\n- Dissolve in 100 mL de PBS (pH pH 7.3) previously heated to around 60 °C.\n- Mix the solution until it completely clears up.\n- Filter and store at 4 °C for a duration of 20160 min.", "[Steps] Permeabilize and block the non-specific pri... |
91,419 | Processing of fixed spheroids for TOBis barcoding, enzyme-free dissociation and antibody staining for CyTOF | 4 | dx.doi.org/10.17504/protocols.io.4r3l22bz4l1y/v1 | https://www.protocols.io/view/processing-of-fixed-spheroids-for-tobis-barcoding-c5h3y38n | Ralitsa R Madsen | TITLE: Processing of fixed spheroids for TOBis barcoding, enzyme-free dissociation and antibody staining for CyTOF
AUTHORS: Ralitsa R Madsen
[DESCRIPTION]
This protocol is an adaptation and extension of the original work on single-cell signalling in organoids by the Tape Lab at UCL. In this adaptation, I have optimise... | ["[Spheroid collection] Generate spheroids in Elplasia plates (96-well or 24-well plate format) according to the following protocol: dx.doi.org/10.17504/protocols.io.3byl4bnrrvo5/v1", "[Spheroid collection] At the end of your experiment, add 16 % formaldehyde straight to the culture medium for a final dilution to 4 % (... |
null | null | null | dx.doi.org/10.17504/protocols.io.hhfb33n | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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68,194 | Centriflaken: an automated data analysis pipeline for assembly and in silico analyses of food-borne pathogens from metagenomic samples | 5 | dx.doi.org/10.17504/protocols.io.kxygxzdbwv8j/v5 | https://www.protocols.io/view/centriflaken-an-automated-data-analysis-pipeline-f-ceuatese | Kranti Konganti, Vishal Thovarai, Meghan Maguire, Julie A. Kase, Narjol Gonzalez-Escalona | TITLE: Centriflaken: an automated data analysis pipeline for assembly and in silico analyses of food-borne pathogens from metagenomic samples
AUTHORS: Kranti Konganti, Vishal Thovarai, Meghan Maguire, Julie A. Kase, Narjol Gonzalez-Escalona
[DESCRIPTION]
Rapid and comprehensive analysis of metagenomic data from any sa... | ["[Create GalaxyTrakr Account and Login] Create an account and Login:\n\nIf you do not already have an account on GalaxyTrakr, please create one by visiting this URL: https://account.galaxytrakr.org/Account/Register", "[Create GalaxyTrakr Account and Login] Once your account is activated, login by visiting https://gala... |
47,895 | Microdialysis guide cannula implantation surgery | 4 | dx.doi.org/10.17504/protocols.io.bszxnf7n | https://www.protocols.io/view/microdialysis-guide-cannula-implantation-surgery-bszxnf7n | Christiana.bjorkli | TITLE: Microdialysis guide cannula implantation surgery
AUTHORS: Christiana.bjorkli
[DESCRIPTION]
Implantation surgery to insert microdialysis guide cannulas (CMA 7; CMA Microdialysis AB, Kista, Sweden) into the lateral ventricle of mice. In animals that are implanted in the lateral ventricle, CSF surfaces shortly a... | ["[Pre-surgery] Habituate animals to food and housing they will receive post-surgery. Check the health status of the animal and autoclave your instruments the day prior to surgery.", "[Preparation of stereotaxic surgery for microdialysis guide implantation] Tidy and clean the surgery table. Disinfect the surgery table ... |
86,837 | Nielsen and Ford (2023) M4-mediated cholinergic transmission is reduced in parkinsonian mice and its restoration alleviates motor deficits and levodopa-induced dyskinesia | 2 | dx.doi.org/10.17504/protocols.io.dm6gp336jvzp/v1 | https://www.protocols.io/view/nielsen-and-ford-2023-m4-mediated-cholinergic-tran-cy2vxye6 | Beatriz E Nielsen, Christopher P Ford | TITLE: Nielsen and Ford (2023) M4-mediated cholinergic transmission is reduced in parkinsonian mice and its restoration alleviates motor deficits and levodopa-induced dyskinesia
AUTHORS: Beatriz E Nielsen, Christopher P Ford
[DESCRIPTION]
This collection contains protocols detailing methods used in Nielsen and Ford (2... | [] |
51,653 | Molecular cloning of SHIP164 plasmids for expression in mammalian cells | 4 | dx.doi.org/10.17504/protocols.io.8epv5z5kjv1b/v1 | https://www.protocols.io/view/molecular-cloning-of-ship164-plasmids-for-expressi-bwpdpdi6 | michael.hanna , Michael G Hanna, Pietri De Camilli | TITLE: Molecular cloning of SHIP164 plasmids for expression in mammalian cells
AUTHORS: michael.hanna , Michael G Hanna, Pietri De Camilli
[DESCRIPTION]
This protocol is to help with the molecular cloning of SHIP164 and the sequences of other proteins.
[BEFORE_START]
We experienced difficulty in amplifying SHIP164 fr... | ["[Cloning strategy] Linearize destination vector using restriction enzyme digest following manufacturers protocol (New England Biolabs).", "[Cloning strategy] Amplify desired insert by PCR making sure to include 15-20 bp overhang homology with destination vector.", "[Cloning strategy] Run both cut vector and PCR produ... |
77,263 | Sidoli Phosphoenrichment From Clean Dry Peptides | 4 | dx.doi.org/10.17504/protocols.io.n2bvj8jxngk5/v1 | https://www.protocols.io/view/sidoli-phosphoenrichment-from-clean-dry-peptides-cpppvmmn | Edwin Yoo | TITLE: Sidoli Phosphoenrichment From Clean Dry Peptides
AUTHORS: Edwin Yoo
[DESCRIPTION]
Sidoli Phosphoenrichment From Clean Dry Peptides
[STEPS]
1. Obtain trypsinized peptides that are clean and dried (ie. completed desalting or S-trap).
2. - Dilute your peptide solution at least 10 times with loading buffer (alt... | ["Obtain trypsinized peptides that are clean and dried (ie. completed desalting or S-trap).", "- Dilute your peptide solution at least 10 times with loading buffer (alternatively if you have 100 μL sample you can add 50 μl water, 50 μL 100% TFA, 800 μL Acetonitrile and 76 mg Glycolic acid to make the sample up to the p... |
86,509 | Electrophysiological recording from a chronic chamber-implanted non-human primate | 4 | null | https://www.protocols.io/view/electrophysiological-recording-from-a-chronic-cham-cyqmxvu6 | Witold J Lipski, Daisuke Kase, Devin R Harsch, Robert S Turner | TITLE: Electrophysiological recording from a chronic chamber-implanted non-human primate
AUTHORS: Witold J Lipski, Daisuke Kase, Devin R Harsch, Robert S Turner
[DESCRIPTION]
This protocol describes the preparation and insertion of extracellular recording electrodes into intracranial targets of a non-human primate imp... | ["[Preparation before the day of recording] Choose the target area using resources such as an MRI or prior brain mapping.", "[Preparation before the day of recording] Calculate the distance from the micro-drive to the surface of the brain.", "[Preparation before the day of recording] Draw a mark on the dura piercing gu... |
88,733 | 13329A - Shoot Maturation Medium | 4 | null | https://www.protocols.io/view/13329a-shoot-maturation-medium-c2v5ye86 | leiboffs | TITLE: 13329A - Shoot Maturation Medium
AUTHORS: leiboffs
[DESCRIPTION]
This is part of the Leiboff Lab maize transformation protocol for somatic embryogenesis of B104 immature embryos. This protocol is a combination of Chen et al. 2022 and Kang et al. 2022 with some modifications based on material availability. This ... | ["[Planning] Estimate the volume of 13329A you will need based on the following:\n\n \n\nMake sure to round up! Check the table below to plan your media", "[Mixing Heat-Stable Ingredients] Retrieve the following heat-stable ingredients:\nMurashige & Skoog Basal Salt Mixture, 'Basal MS' - Stored in Main Lab, 4C Refrige... |
61,681 | Preparation of agarose pads suitable for viewing filamentous cyanobacterial microbial communities using time-lapse imaging | 1 | dx.doi.org/10.17504/protocols.io.81wgb65p1lpk/v1 | https://www.protocols.io/view/preparation-of-agarose-pads-suitable-for-viewing-f-b8grrtv6 | Jerko Rosko, Mary Coates, Kelsey Cremin, Christian Zerfass, Orkun Soyer | TITLE: Preparation of agarose pads suitable for viewing filamentous cyanobacterial microbial communities using time-lapse imaging
AUTHORS: Jerko Rosko, Mary Coates, Kelsey Cremin, Christian Zerfass, Orkun Soyer
[DESCRIPTION]
This protocol is for viewing cultures on top of agar pads, e.g filamentous cyanobacterial mi... | ["[STEP 1: Agarose pad medium (makes approx. 50 pads)] Into a 100 mL Duran bottle, add 1 g agarose and make up to 47.35 mL with DW.", "[STEP 1: Agarose pad medium (makes approx. 50 pads)] Autoclave at 120 °C for 20 – 30 minutes. Remove at 80 °C.", "[STEP 1: Agarose pad medium (makes approx. 50 pads)] After autoclaving... |
30,096 | Low Cell Input Nuclei Isolation for Single Cell ATAC-Seq | 1 | dx.doi.org/10.17504/protocols.io.bp2l6n1xkgqe/v1 | https://www.protocols.io/view/low-cell-input-nuclei-isolation-for-single-cell-at-9mqh45w | Carmen Sancho | TITLE: Low Cell Input Nuclei Isolation for Single Cell ATAC-Seq
AUTHORS: Carmen Sancho
[DESCRIPTION]
This protocol describes the the methodology of nuclei isolation for Single Cell ATAC Sequencing adopted from 10X Genomics guide CG000169 Revision D.
[STEPS]
SECTION: Prepare diluted nuclei buffer
1.
Keep nuclei buff... | ["[Prepare diluted nuclei buffer] Keep nuclei buffer on ice!", "[Prepare buffer A] Keep buffer A on ice and prepare fresh!", "[Prepare wash buffer] Keep wash buffer on ice and prepare fresh!", "[Additional buffers] PBS + 0.04% BSA (maintain at 4 °C )", "[Nuclei isolation from fresh cells] Nuclei may be isolated from 20... |
95,183 | White-rot fungi aromatic catabolic intermediates analyzed by HPLC-DAD | 1 | dx.doi.org/10.17504/protocols.io.n92ldmkpol5b/v1 | https://www.protocols.io/view/white-rot-fungi-aromatic-catabolic-intermediates-a-c87pzzmn | William E. Michener, Sean P. Woodworth, Stefan J. Haugen, Morgan A. Ingraham, Kelsey J. Ramirez, Gregg T. Beckham, Davinia Salvachúa | TITLE: White-rot fungi aromatic catabolic intermediates analyzed by HPLC-DAD
AUTHORS: William E. Michener, Sean P. Woodworth, Stefan J. Haugen, Morgan A. Ingraham, Kelsey J. Ramirez, Gregg T. Beckham, Davinia Salvachúa
[DESCRIPTION]
An analysis method was developed for the quantitation of catabolic intermediates produ... | ["[Preparation of standards] Calibration curve", "[Analytical quality control] Multiple strategies are utilized when performing this analysis to ensure instrument stability and reproducibility.", "[Preparation of standards] Standards\n\nThis procedure for standard preparation is previously documented in our work publis... |
94,428 | An NGS amplicon tiling protocol for HIV-1 drug resistance detection using Illumina® COVIDSeq™ Assay Kit | 4 | dx.doi.org/10.17504/protocols.io.n92ldmq4ol5b/v3 | https://www.protocols.io/view/an-ngs-amplicon-tiling-protocol-for-hiv-1-drug-res-c8f4ztqw | Noah C. Hull, Eugene Yeboah, Laura Tsaknaridis, Vanda Makris | TITLE: An NGS amplicon tiling protocol for HIV-1 drug resistance detection using Illumina® COVIDSeq™ Assay Kit
AUTHORS: Noah C. Hull, Eugene Yeboah, Laura Tsaknaridis, Vanda Makris
[DESCRIPTION]
Summary
Human immunodeficiency virus (HIV) is the pathogen responsible for acquired immunodeficiency syndrome (AIDS) and c... | ["Sample Extraction\n\nHIV-1 subtype B positive culture control ZeptoMetrix (Part #v0801032CF), was extracted via the Qiagen Advanced XL DSP kit on the EZ1 extractor and serially diluted to the following concentration: 10ᶺ(-1), 10ᶺ(-2), 10ᶺ(-3), 10ᶺ(-4), 10ᶺ(-5), and 10ᶺ(-6), Undiluted control (1.74*10^10 IU/mL or 2.09... |
41,906 | Testing platelet aggregation activity | 1 | dx.doi.org/10.17504/protocols.io.bk6skzee | https://www.protocols.io/view/testing-platelet-aggregation-activity-bk6skzee | Jamilya Mansurova , Ludmila Karazhanova, Aisulu Zhunuspekova | TITLE: Testing platelet aggregation activity
AUTHORS: Jamilya Mansurova , Ludmila Karazhanova, Aisulu Zhunuspekova
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Aggregatometry is based on the ability of platelets to activate and form cell aggregates under the influence of inductors. During the an... | ["Whole blood samplingBlood sampling was performed in 12-48 hours after PCI in the morning on an empty stomach from the cubital vein into vacuum tubes with 3.8% sodium citrate (in a ratio of 9: 1) with short-term application of a tourniquet and with 0.8 mm. diameter needle. The blood samples were delivered to the labor... |
38,262 | Cross-linking of IgG to Protein A or G Beads (S1425/S1430) | 1 | dx.doi.org/10.17504/protocols.io.bhkwj4xe | https://www.protocols.io/view/cross-linking-of-igg-to-protein-a-or-g-beads-s1425-bhkwj4xe | New England Biolabs | TITLE: Cross-linking of IgG to Protein A or G Beads (S1425/S1430)
AUTHORS: New England Biolabs
[DESCRIPTION]
This protocol consists of an IgG purification step followed by covalent cross-linking of the IgG to the Protein A/G solid support. For IgG that has been previously purified, proceed directly to the cross-lin... | ["[IgG Immobilization] Vortex and thoroughly resuspend Protein A Magnetic Beads.", "[IgG Immobilization] Aliquot 100 µL to a sterile microcentrifuge tube.", "[IgG Immobilization] Add 500 µL and vortex to resuspend. Apply magnet for 30 s, to pull beads to the side of the tube and remove supernatant. (Wash 1/2)", "[IgG I... |
null | null | null | dx.doi.org/10.17504/protocols.io.nmpdc5n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes the literature search for a systematic review on the educational impact of Mini-CEX and DOPS.</p>
[STEPS]
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null | null | null | dx.doi.org/10.17504/protocols.io.egkbbuw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in the protocol "<a href="https://www.protocols.io/view/Large-Volume-Marine-Cyanophage-Phage-Protocols-c3iykd" target="_blank">Large Volume Marine Cyanophage protocols</a><span data-sheets-value="[null,2,"Large Volume Marine Cyanophage protocols"]" data-sheets-... | [] |
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