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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38,662 | Generalized mathematical model of cancer heterogeneity | 4 | dx.doi.org/10.17504/protocols.io.bhzej73e | https://www.protocols.io/view/generalized-mathematical-model-of-cancer-heterogen-bhzej73e | Motohiko Naito | TITLE: Generalized mathematical model of cancer heterogeneity
AUTHORS: Motohiko Naito
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The number of reports on mathematical modeling related to oncology is increasing with advances in oncology. Even though the field of oncology has developed significan... | ["There's a short protocol available that contains all used codes, and a detailed version that is based on the preprint.", "[Mathematical modeling of cancerous tumor growth]\nThe growth of cancer is assumed mathematically to follow the Poisson process with parameter λ.", "[Mathematical modeling of cancerous tumor growt... |
null | null | null | dx.doi.org/10.17504/protocols.io.jvxcn7n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes a method of sampling groundwater from bore-holes. The method was used in my PhD research on aquifer microbial ecology over two weeks at the Wellington Research Station in New South Wales, Australia. With a little practise, the method can probably be ca... | [] |
22,437 | 01: Introduction to Unix | null | dx.doi.org/10.17504/protocols.io.z6df9a6 | null | Frank Aylward | TITLE: 01: Introduction to Unix
AUTHORS: Frank Aylward
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [start]
A Unix or Unix-like operating system generally has a wide variety of build-in functions that are extremely useful for navigating between folders, exploring the contents of files, and getting vario... | ["[start]\nA Unix or Unix-like operating system generally has a wide variety of build-in functions that are extremely useful for navigating between folders, exploring the contents of files, and getting various summary statistics that are useful before undertaking a bioinformatic analysis. Here we will explore some of t... |
90,333 | 813.1 Multiplexed Immunofluorescence Phenocycler-Fusion® Imaging of FFPE Lung Sections | 4 | dx.doi.org/10.17504/protocols.io.6qpvr38dpvmk/v2 | https://www.protocols.io/view/813-1-multiplexed-immunofluorescence-phenocycler-f-c4f5ytq6 | Jeffrey Purkerson, Gloria S Pryhuber, Luis Colon, Heidie Huyck | TITLE: 813.1 Multiplexed Immunofluorescence Phenocycler-Fusion® Imaging of FFPE Lung Sections
AUTHORS: Jeffrey Purkerson, Gloria S Pryhuber, Luis Colon, Heidie Huyck
[DESCRIPTION]
This protocol describes multiplexed immunofluorescent (MxF) staining and imaging of FFPE lung tissue sections utilizing the Phenocycler-Fu... | ["[Lung section preparation] Bake Sections to promote tissue adherence to the slide.\nSince stained slides can be stored in storage buffer for a maximum 5 days without diminution of staining signal intensity, and Phenocycler-Fusion imaging typically ranges from 16-24h, staining more than 5 slides at a time is not reco... |
null | null | null | dx.doi.org/10.17504/protocols.io.s7fehjn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The description and identification of metabolites using Gas Chromatography - Mass Spectrometry (GC-MS) is a powerful tool to study the cnidarian-dinoflagellate symbiosis. The applications range from first descriptions of metabolite profiles to the identification of specific m... | [] |
104,692 | Bravo workstation: automated single-stranded DNA library preparation (ssDNA2.0) | 4 | dx.doi.org/10.17504/protocols.io.kqdg32bdpv25/v1 | https://www.protocols.io/view/bravo-workstation-automated-single-stranded-dna-li-digu4bww | Sarah Nagel, Anna Schmidt, Ayinuer Aximu Petri, Anya Patova, Merlin Szymanski, Elena Essel, Matthias Meyer | TITLE: Bravo workstation: automated single-stranded DNA library preparation (ssDNA2.0)
AUTHORS: Sarah Nagel, Anna Schmidt, Ayinuer Aximu Petri, Anya Patova, Merlin Szymanski, Elena Essel, Matthias Meyer
[DESCRIPTION]
We here provide an implementation of the ssDNA2.0 single-stranded library preparation method (Gansauge... | ["[Reagent and sample preparation (days/weeks/months before the run)] Prepare master mixes (Desphosphorylation mix, Adapter/splinter mix, Ligation mix I, Fill-in mix, Klenow mix, Ligation mix II) and aliquots of library positive controls (LPCs), library negative controls (LNCs) and if needed positive text extracts (PTE... |
20,447 | Picking Clones | null | dx.doi.org/10.17504/protocols.io.x77frrn | null | Celeste Karch, Rita Martinez, Jacob Marsh | TITLE: Picking Clones
AUTHORS: Celeste Karch, Rita Martinez, Jacob Marsh
[STEPS]
?. Coat 96 well plate with 50 μl Matrigel per well.
?. Incubate at for .
?. Prior to picking, aspirate Matrigel. Replace with mTesR1 + 10 μM Rock Inhibitor.
50 µl
?. Using p20, pick individual clones and place into unique wells. Use a n... | ["Coat 96 well plate with 50 μl Matrigel per well.", "Incubate at for .", "Prior to picking, aspirate Matrigel. Replace with mTesR1 + 10 μM Rock Inhibitor.\n50 µl", "Using p20, pick individual clones and place into unique wells. Use a new tip with each clone.", "Incubate at overnight.", "Change media daily (150 μl mT... |
64,424 | pellamore (Scam or Legit?) Effective Formula or Cheap Brand? | 3 | dx.doi.org/10.17504/protocols.io.bp2l61y5dvqe/v1 | https://www.protocols.io/view/pellamore-scam-or-legit-effective-formula-or-cheap-ca6gshbw | fluxactive | TITLE: pellamore (Scam or Legit?) Effective Formula or Cheap Brand?
AUTHORS: fluxactive
[DESCRIPTION]
• Price - Visit Official Website
[STEPS] | [] |
68,510 | Miniprep (NEB Monarch) (Instructor protocol) | 4 | null | https://www.protocols.io/view/miniprep-neb-monarch-instructor-protocol-ce56tg9e | Brian Teague | TITLE: Miniprep (NEB Monarch) (Instructor protocol)
AUTHORS: Brian Teague
[DESCRIPTION]
This is the instructor protocol for
[GUIDELINES]
The "pick colonies" part is in the instructor protocol because it needs to happen ~16-20 hours before the lab. (I suppose it would be possible to ask students to come in the p... | ["[Prepare LB broth] Fill a 1 liter screw-cap bottle with approximately 900 mL of deionized water.", "[Prepare LB broth] Add:\n5 g \n10 g \n10 g", "[Prepare LB broth] Add water to a total volume of 1 L (eyeballing is OK, no need to dirty a graduated cylinder). Cap and shake to mix.", "[Prepare LB broth] Loosen the ... |
14,788 | Human Islet Cryopreservation | null | dx.doi.org/10.17504/protocols.io.spcediw | null | James Lyon, Patrick MacDonald, Jocelyn Manning Fox | TITLE: Human Islet Cryopreservation
AUTHORS: James Lyon, Patrick MacDonald, Jocelyn Manning Fox
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details the cryopreservation of human islets, as performed by the Alberta Diabetes Institute IsletCore. Human islets cryopreserved using this ... | ["[Pre-cool cryopreservation bath]\nPre-cool FTS bath and set temperature at –7.4°C starting temp approximately 2 hours prior beginning the cryopreservation.", "[Protocol - Step 1]\nAliquot islets into the cryopreservation tubes with a maxiumum of 25,000 IEQ per cryopreservation tube.", "[Label the cryopreservation tub... |
58,819 | Q5® Site-Directed Mutagenesis - CHEM 384/584 | 1 | null | https://www.protocols.io/view/q5-site-directed-mutagenesis-chem-384-584-b5pbq5in | New England Biolabs | TITLE: Q5® Site-Directed Mutagenesis - CHEM 384/584
AUTHORS: New England Biolabs
[DESCRIPTION]
The Q5 Site-Directed Mutagenesis Kit (Without Competent Cells) enables rapid, site-specific mutagenesis of double-stranded plasmid DNA in less than 2 hours (Figure 1). The kit utilizes the robust Q5 Hot Start High-Fidelit... | ["[Exponential Amplification (PCR)] Assemble the following reagents in a thin-walled PCR tube:\n 25 μl RXN FINAL CONC. Q5 Hot Start High-Fidelity 2X Master Mix 12.5 μl 1X 10 μM Forward Primer 1.25 μl 0.5 μM 10 μM Reverse Primer 1.25 μl 0.5 μM Template DNA (1–25 ng/μl) 1 μl 1-25 ng Nuclease-free water 9.0 ... |
9,113 | Top2 inhibitor sensitivity | null | dx.doi.org/10.17504/protocols.io.k5zcy76 | null | Jacob Kirkland | TITLE: Top2 inhibitor sensitivity
AUTHORS: Jacob Kirkland
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for Top2i sensitivity in attached cells in 96-well format. Short term exposure to Top2i (~3 days)</div></div>
[STEPS]
?. Plate (2) 6cm dishes at 25% confluency (approx. 500K cells). Le... | ["Plate (2) 6cm dishes at 25% confluency (approx. 500K cells). Let attach overnight", "[Induction of shRNAs]\nAdd 1000x Doxycyclin to 1 plate of cells with fresh media and induce for 72 hours changing media with fresh doxycyclin daily. Also change media to corresponding non-induced plate", "[In 96-well plates]\nSplit c... |
65,484 | Chana's | 1 | null | https://www.protocols.io/view/chana-39-s-cb7ksrkw | krausfri | TITLE: Chana's
AUTHORS: krausfri
[DESCRIPTION]
jkl;ajsdklfj
[STEPS] | [] |
44,657 | Isolation of Stromal Vascular Fraction (SVF) from mouse brown adipose tissue (BAT) for single cell RNA-seq | 4 | dx.doi.org/10.17504/protocols.io.bpurmnv6 | https://www.protocols.io/view/isolation-of-stromal-vascular-fraction-svf-from-mo-bpurmnv6 | Farnaz Shamsi, Yu-Hua Tseng | TITLE: Isolation of Stromal Vascular Fraction (SVF) from mouse brown adipose tissue (BAT) for single cell RNA-seq
AUTHORS: Farnaz Shamsi, Yu-Hua Tseng
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines the procedure for the isolation of the Stromal Vascular Fraction (SVF) from mo... | ["Sacrifice the mouse.", "Spray the animal extensively with 70 % EtOH and RNaseZap™.", "Dissect interscapular brown adipose tissue (BAT). If tissues from multiple animals are being dissected, store them in HBSS until all of them are dissected.", "Mince the tissue to very fine pieces in a 50 ml Falcon tube. Add for each... |
99,532 | USDA LTAR Common Experiment measurement: Non-crop plant biodiversity | 0 | dx.doi.org/10.17504/protocols.io.kxygxyzbzl8j/v1 | https://www.protocols.io/view/usda-ltar-common-experiment-measurement-non-crop-p-ddfk23kw | Elizabeth H. Boughton, Grégory Sonnier | TITLE: USDA LTAR Common Experiment measurement: Non-crop plant biodiversity
AUTHORS: Elizabeth H. Boughton, Grégory Sonnier
[DESCRIPTION]
Non-crop plant diversity, implemented by producers to manage environmental quality or biodiversity-based ecosystem services within croplands, is important because it is strongly ... | ["[Sample collection, processing, and analysis] Number of Whittaker plots: We recommend a minimum of three plots per plant community at a given site, but plot number determination varies among sites based on the number of communities, available labor, and other constraints.", "[Sample collection, processing, and analys... |
63,332 | K1 Keto Reviews : Ingredients,Price, Reviews & Discount Offers! | 1 | dx.doi.org/10.17504/protocols.io.kxygxz1jdv8j/v1 | https://www.protocols.io/view/k1-keto-reviews-ingredients-price-reviews-amp-disc-b94cr8sw | roxyhiml | TITLE: K1 Keto Reviews : Ingredients,Price, Reviews & Discount Offers!
AUTHORS: roxyhiml
[DESCRIPTION]
➢ Product Name ⮞K1 Keto Reviews
➢ Composition ⮞Natural Organic Compound
➢ Side-Effects ⮞ NA
➢ Availability ⮞ Online
➢ Rating ⮞⭐⭐⭐⭐⭐
➢ Official Website⮞>>>K1KetoLife.com
➤ Price (for Sale) Buy Now Here
➤ Price (... | ["[K1 Keto Reviews] This keto diet will also leave you feeling vibrant, active, and full of energy thanks to its low calorie and high nutrient content. However, getting your body into a state of ketosis might be difficult. And most of us don’t have the time to meticulously follow all of the keto diet’s steps. This is w... |
92,565 | Opentrons Dual-Index Primer Plate Workflow | 1 | null | https://www.protocols.io/view/opentrons-dual-index-primer-plate-workflow-c6mvzc66 | Stephen Douglas Russell | TITLE: Opentrons Dual-Index Primer Plate Workflow
AUTHORS: Stephen Douglas Russell
[DESCRIPTION]
This protocol is designed to utilize the Opentrons robotic automation platform to generate dual-index primer - master mix plates for PCR reactions for NGS, particularly for DNA barcoding large specimen pools with Oxford Na... | ["[Initial Prep] Starting Point – 1 Stock Primer Plate with 96 different ONT-tagged primers. At least 90uL fluid at 100uM concentration. Spin down this plate. Transfer liquid to a BioRad 200uM plate. If you have less than 90uL in any of the cells, you will need to make modifications to the programs.", "[OT-2 "Work... |
85,986 | CRISPR tagging of the TMEM192 gene with 3xHA in H9 ES AAVS-NGN2 cells for Lyso-IP | 1 | dx.doi.org/10.17504/protocols.io.e6nvwdjd7lmk/v1 | https://www.protocols.io/view/crispr-tagging-of-the-tmem192-gene-with-3xha-in-h9-cx8axrse | Jiuchun Zhang, Harper JW, Sharan Sharan Swarup | TITLE: CRISPR tagging of the TMEM192 gene with 3xHA in H9 ES AAVS-NGN2 cells for Lyso-IP
AUTHORS: Jiuchun Zhang, Harper JW, Sharan Sharan Swarup
[DESCRIPTION]
This protocol describes a method for knockin of a 3X HA tag onto the C-terminus of the TMEM192 gene in human H9 ES AAVS1-NGN2 cells using CAS9 and a homologous ... | ["[preparing Cas9 RNP complex for electroporation] Add 10 µL to a sterile 1.5 ml tube. Add 6 µg. Then add 1.2 µg and 1 microgram TMEM192-3xHA homology arm plasmid (Addgene#175777). Pipet up and down to mix. Let it sit at Room temperature for 10 min. This is enough for 2 transfections (== one 6 well).", "[preparing Cas9... |
null | null | null | dx.doi.org/10.17504/protocols.io.m6mc9c6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Flow Cytometry<br /><br /></p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
20,230 | U Mass - Hyperinsulinemic-euglycemic clamp | null | dx.doi.org/10.17504/protocols.io.xzefp3e | null | Jason Kim | TITLE: U Mass - Hyperinsulinemic-euglycemic clamp
AUTHORS: Jason Kim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">Hyperinsulinemic-euglycemic clamp is the gold-standard method to assess insulin sensitivity. The hype... | ["Survival surgery is performed to establish a chronic indwelling catheter at 5~6 days prior to experiment for intravenous infusion. (refer to M1023: Surgery-jugular vein cannulation)", "Mice are fasted overnight (~15 hours) or for 5 hours prior to the start of experiment.", "Place a mouse in a rat-size restrainer wit... |
null | null | null | dx.doi.org/10.17504/protocols.io.krncv5e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This simple and rapid chromatographic detection method was developed and validated in order to accurately quantify trace levels of free gossypol in different cotton materials, including cottonseed, cottonseed cake and cottonseed cake treated with macrofungi.</p>
[BEFORE_STAR... | [] |
31,411 | Fluorescence Titering Assay for Lentivirus | null | dx.doi.org/10.17504/protocols.io.bawtifen | null | Addgene the Nonprofit Plasmid Repository | TITLE: Fluorescence Titering Assay for Lentivirus
AUTHORS: Addgene the Nonprofit Plasmid Repository
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is for running a fluorescence titering assay for lentivirus. To see the full abstract and additional resources, visit the </span><a ... | ["[Seeding cells]\nSeed 75,000 cells into each well of a 6-well dish.", "[Seeding cells]\nDilute 525,000 cells into of DMEM complete.\n14 ml", "[Seeding cells]\nMix well by pipetting or inverting.", "[Seeding cells]\nAliquot of cell suspension into each well of the 6-well dish.\n2 ml", "[Seeding cells]\nIncubate the ... |
88,871 | Human Adipose Dissociation and Cell Culture -- University of Minnesota TMCs | 1 | dx.doi.org/10.17504/protocols.io.eq2lyj8jmlx9/v1 | https://www.protocols.io/view/human-adipose-dissociation-and-cell-culture-univer-c22fygbn | Elizabeth Thompson, Laura J Niedernhofer, David A Bernlohr | TITLE: Human Adipose Dissociation and Cell Culture -- University of Minnesota TMCs
AUTHORS: Elizabeth Thompson, Laura J Niedernhofer, David A Bernlohr
[DESCRIPTION]
Purpose: To dissociate human adipose to obtain adipose progenitors and endothelial cells for cell culture experiments.
Adapted from Miltenyi Biotec -... | ["[I. Materials] Adipose Tissue Dissociation Kit mouse and rat (Miltenyi Biotec; 130-105-808)\nKit Components: 5 vials containing:\n2 vials of Enzyme D (lyophilized powder)\n1 vial of Enzyme R (lyophilized powder)\n1 vial of Enzyme A (lyophilized powder)\n1 mL of Buffer A", "[I. Materials] Fibroblast Media (made ahead ... |
87,478 | Imaging of gene expression in single cells by visualizing mRNA using HCR-FISH v3.0 on filtered cells from marine sediment | 4 | null | https://www.protocols.io/view/imaging-of-gene-expression-in-single-cells-by-visu-cznwx5fe | Ranjani Murali, Victoria J Orphan | TITLE: Imaging of gene expression in single cells by visualizing mRNA using HCR-FISH v3.0 on filtered cells from marine sediment
AUTHORS: Ranjani Murali, Victoria J Orphan
[DESCRIPTION]
The purpose of this protocol is to visualize gene expression in single cells by targeting the mRNA of genes of interest using HCR-FIS... | ["[Density separation of ANME-SRB aggregates from sediment] Incubate at 60 °C for 3 min, in a heating block.", "[Density separation of ANME-SRB aggregates from sediment] Take 50 µL of sediment slurry in a 2mL Eppendorf tube. Add 850 µL TE Buffer ( 1M Tris, 0.1 M EDTA, pH 8) and 100 µL 100 µM pyrophosphate.", "[Density... |
88,552 | Colony PCR | 4 | dx.doi.org/10.17504/protocols.io.5jyl8pex8g2w/v1 | https://www.protocols.io/view/colony-pcr-c2qgydtw | NUS iGEM | TITLE: Colony PCR
AUTHORS: NUS iGEM
[DESCRIPTION]
2023 NUS-Singapore iGEM team followed this protocol to perform preliminary screening of plasmid-containing colonies without the need for overnight cell culture. This screening aimed to confirm the correct assembly of DNA fragments during Gibson Assembly or the presence... | ["Circle the colony of interest.", "Run a PCR with the setting below:", "After the PCR is complete, proceed to run gel electrophoresis for the samples.", "Prepare the mixture below in a PCR tube, the final volume is 50 µL:", "Mix the solution well by vortexing the tubes and then split the solution equally into 5 new PC... |
59,445 | JAX - Nuclei Isolation for 10x Genomics A | 1 | dx.doi.org/10.17504/protocols.io.ewov1n9npgr2/v1 | https://www.protocols.io/view/jax-nuclei-isolation-for-10x-genomics-a-b6avrae6 | William F Flynn, Elise Courtois, Greggory A Perry, Sandra L Daigle, Paul Gabriel, Diane Luo, Jessica Grassmann | TITLE: JAX - Nuclei Isolation for 10x Genomics A
AUTHORS: William F Flynn, Elise Courtois, Greggory A Perry, Sandra L Daigle, Paul Gabriel, Diane Luo, Jessica Grassmann
[DESCRIPTION]
The purpose of this protocol is to produce single nuclei from frozen human tissues for downstream assaying with the 10x Genomics Multio... | ["[Sample Prep] Slightly thaw sample out on ice and place onto pre chilled Petri dish on ice.", "[Sample Prep] Cut tissue into small pieces and add to a microcentrifuge tube.", "[Cell lysis] In micro centrifuge tube containing the tissue add 100 µL of lysis buffer.", "[Cell lysis] Using a plastic pestle to grind tissue... |
47,073 | Aqueous adenine solution preparation | 1 | null | https://www.protocols.io/view/aqueous-adenine-solution-preparation-br79m9r6 | seifip | TITLE: Aqueous adenine solution preparation
AUTHORS: seifip
[DESCRIPTION]
Aqueous adenine solution preparation
[STEPS]
8.
SECTION: Prepare a 10 mM adenine solution in water as follows:
1. Weigh out 0.13513 g of adenine.
SECTION: Prepare a 10 mM adenine solution in water as follows:
2. Transfer the adenine to ... | ["[Prepare a 10 mM adenine solution in water as follows:] Weigh out 0.13513 g of adenine.", "[Prepare a 10 mM adenine solution in water as follows:] Transfer the adenine to an Erlenmeyer flask and add an appropriate solvent like distilled water or a biological buffer (amount of solvent will depend on desired final conc... |
101,135 | DENV2 NS2B-NS3 protease co-expression construct small scale expression and purification protocol | 1 | dx.doi.org/10.17504/protocols.io.rm7vzj362lx1/v2 | https://www.protocols.io/view/denv2-ns2b-ns3-protease-co-expression-construct-sm-dezp3f5n | Korvus Wang, michael fairhead, Eleanor Williams | TITLE: DENV2 NS2B-NS3 protease co-expression construct small scale expression and purification protocol
AUTHORS: Korvus Wang, michael fairhead, Eleanor Williams
[DESCRIPTION]
This protocol details the co-expression and purification of DENV2 NS2B-NS3 protease construct bearing a N-terminal His-GST tag at small scale (<... | ["[Plasmid Transformation] DVNS2B3 N-terminal His-GST tagged co-expression construct was inoculated from its BL21(DE3)-RR glycerol stock.", "[Protein expression] When the OD600 approximately 1.8, add 1mM IPTG. Lower the temperature and shaker speed to . Incubate overnight.", "[Protein Purifcation] Perform IMAC to extr... |
90,279 | TEM | 1 | dx.doi.org/10.17504/protocols.io.q26g7pd79gwz/v1 | https://www.protocols.io/view/tem-c4efytbn | Alexander Röntgen | TITLE: TEM
AUTHORS: Alexander Röntgen
[DESCRIPTION]
TEM protocol.
[STEPS]
SECTION: Preparation
1. Recover samples by pipetting out of aggregation plate
SECTION: Preparation
2. Glow-discharge grids (3-mm 300-mesh (EM Resolutions Ltd))
SECTION: Sample spotting and staining
3. Take up grid with tweezers
SECTION: Sample ... | ["[Preparation] Recover samples by pipetting out of aggregation plate", "[Preparation] Glow-discharge grids (3-mm 300-mesh (EM Resolutions Ltd))", "[Sample spotting and staining] Take up grid with tweezers", "[Sample spotting and staining] Spot 2.3 µL sample on grid", "[Sample spotting and staining] Stain sample with 2... |
43,742 | Microinjection Techniques in Fly Embryos to Study the Function and Dynamics of SMC Complexes | 4 | dx.doi.org/10.17504/protocols.io.bnx6mfre | https://www.protocols.io/view/microinjection-techniques-in-fly-embryos-to-study-bnx6mfre | Catarina Carmo, Margarida Araújo, Raquel Oliveira | TITLE: Microinjection Techniques in Fly Embryos to Study the Function and Dynamics of SMC Complexes
AUTHORS: Catarina Carmo, Margarida Araújo, Raquel Oliveira
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Structural maintenance of chromosomes (SMC) proteins are critical to maintain mitotic fidelit... | ["[Collecting and Preparing Embryos for Live Imaging]\nSet up a cage with the fly strain of your choosing. Use an apple juice plate with a smear of fresh yeast paste at the bottom of the cage.\nWhen setting a cage, take into consideration that older flies have a decreased egg-laying capacity. Males that have matured fo... |
null | null | null | dx.doi.org/10.17504/protocols.io.m6jc9cn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p align="LEFT"><span style="font-family: Arial-BoldMT; font-size: small;">Lipofectamine</span><span style="font-family: Arial-BoldMT; font-size: xx-small;">™ </span><span style="font-family: Arial-BoldMT; font-size: small;">2000 Transfection Protocol</span></p>
<p align="LEFT">... | [] |
74,966 | Basic pipet technique training | 6 | dx.doi.org/10.17504/protocols.io.36wgqjo4yvk5/v1 | https://www.protocols.io/view/basic-pipet-technique-training-cmfwu3pe | Ying-Yu Hu | TITLE: Basic pipet technique training
AUTHORS: Ying-Yu Hu
[DESCRIPTION]
Here we adopt the molybdate colorimetric reaction from our Total particulate phosphorus (TPP) measurement as a training material for our new lab members to learn basic pipetting technique.
[STEPS]
SECTION: Preparing standard working solu... | ["[Preparing standard working solutions] Date:\n\nTrainee:", "[Prepare working reagents] 2.5 % ammonium molybdate reagent", "[Prepare working reagents] Use graduated cylinder, measure and transfer 6 mL 2.5 % ammonium molybdate reagent into the sulfuric acid tube.", "[Colorimetric measurement] Preheat incubator/shaker ... |
59,514 | DEMoNS protocol for measurement and analysis of eye movements | 1 | null | https://www.protocols.io/view/demons-protocol-for-measurement-and-analysis-of-ey-b6c2raye | Jenny Nij Bijvank | TITLE: DEMoNS protocol for measurement and analysis of eye movements
AUTHORS: Jenny Nij Bijvank
[DESCRIPTION]
For questions, send an email to info.demonsprotocol@gmail.com or vanrijn@amsterdamumc.nl
The complete protocol and instructions on measurement and analysis of eye movements with the DEMoNS protocol.
Quantita... | ["[Protocols and instructions] Measurement and analysis protocol, and instructions on analysis and import files in Matlab.\n\nThe Eyelink measurement is created in the Experiment software of SR research and can therfore only be used with an Eyelink (SR Research) eyetracker. These zipped files contain the folders of the... |
null | null | null | dx.doi.org/10.17504/protocols.io.dbm2k5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in <a href="https://www.protocols.io/view/DNase-I-Treatment-c3myk5" target="_blank">DNase I Treatment</a> protocol for DNase inactivation.
[GUIDELINES]
Note: EDTA tetrasodium salt dihydrate is somewhat more soluble and can be made more easily to 1.5M. FW is slightly mor... | [] |
77,259 | Brainless S-trap Proteomics Protocol Mini Columns or 96 well | 4 | dx.doi.org/10.17504/protocols.io.n92ldpj99l5b/v1 | https://www.protocols.io/view/brainless-s-trap-proteomics-protocol-mini-columns-cppjvmkn | Edwin Yoo | TITLE: Brainless S-trap Proteomics Protocol Mini Columns or 96 well
AUTHORS: Edwin Yoo
[DESCRIPTION]
Brainless S-trap Proteomics Protocol Mini Columns or 96 well
[STEPS]
SECTION: Solubilize In SDS, reduce, alkylate
2. Add 50 μL 1X lysis buffer with reductant and alkylator (heated to 99C) to tissue or pelleted cells. ... | ["[Solubilize In SDS, reduce, alkylate] Add 50 μL 1X lysis buffer with reductant and alkylator (heated to 99C) to tissue or pelleted cells. Tissue/cells should be greater than 300 ug.", "[Solubilize In SDS, reduce, alkylate] Measure protein concentration with BCA. Make sure final sample has 1-300 ug protein in 50 ul of... |
52,688 | Minimal important difference in SD units | 1 | dx.doi.org/10.17504/protocols.io.bxpqpmmw | https://www.protocols.io/view/minimal-important-difference-in-sd-units-bxpqpmmw | Yasushi Tsujimoto | TITLE: Minimal important difference in SD units
AUTHORS: Yasushi Tsujimoto
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The current study aims first to describe the anchor-based minimal important difference (MID) estimates in standard deviation (SD) units and then to examine if the robustness of... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.c8mzu5 | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
Glue the flies on hooks, put them into the single-fly valves and give them sugar and water to survive the night. Store them at the appropriate temperature.
[GUIDELINES]
<p><strong>The day before the measurement:<br /></strong>Glue the flies on hooks, put them into the single-f... | [] |
94,139 | Immunophenotyping of immune cells by high dimensional flow cytometry | 4 | dx.doi.org/10.17504/protocols.io.n2bvj3w2plk5/v1 | https://www.protocols.io/view/immunophenotyping-of-immune-cells-by-high-dimensio-c763zrgn | mariangela.massarocenere, Valerio Chiurchiù | TITLE: Immunophenotyping of immune cells by high dimensional flow cytometry
AUTHORS: mariangela.massarocenere, Valerio Chiurchiù
[DESCRIPTION]
Protocol to assess cellular phenotypes by multiparametric flow cytometry panels containing markers to identify cell types and activation states
[STEPS]
SECTION: Tissue disso... | ["[Tissue dissociation] After animal sacrifice (see protocol “intracardiac perfusion”), the dissected and collected cerebral region of interest (SNpc and striatum) is immersed in D-PBS with high glucose buffer at 4°C", "[Tissue dissociation] Immediately after, the brain regions are dissociated to single-cell suspension... |
33,678 | Live/Dead qPCR of B. pertussis IS481 | null | dx.doi.org/10.17504/protocols.io.bc5niy5e | null | Iain MacArthur, Stacy Ramkissoon, Andrew Preston | TITLE: Live/Dead qPCR of B. pertussis IS481
AUTHORS: Iain MacArthur, Stacy Ramkissoon, Andrew Preston
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes the use of qPCR for the quantitative determination of live </span><span style = "font-style:italic;">B. pertussis</span>... | ["[PMA treatment]\nPellet fresh samples by centrifuging at 2,000 x g for 10 minutes and resuspend in 1.2 ml of PBS.", "[PMA treatment]\nTransfer 200µl of resuspended sample into two clear microfuge tubes (continue with 1 sample to Step #3 and 1 sample skip to Step #4).", "[PMA treatment]\nAdd 0.5µl of PMA to one of the... |
88,484 | Plasmid Extraction (Plasmid Isolation) | 4 | dx.doi.org/10.17504/protocols.io.yxmvm3yq6l3p/v1 | https://www.protocols.io/view/plasmid-extraction-plasmid-isolation-c2ncydaw | NUS iGEM | TITLE: Plasmid Extraction (Plasmid Isolation)
AUTHORS: NUS iGEM
[DESCRIPTION]
2023 NUS-Singapore iGEM team followed this protocol to isolate the plasmid from the cells.
[BEFORE_START]
Glycerol stock (900 µL of cell stock in 300 µL of 100% glycerol solution) may be prepared and keep it in the -80 °C fridge before the ... | ["[Cell Culture] Incubate the cells containing the plasmid of interest in a Falcon tube with 5 mL of LB media and 5 µL of the appropriate antibiotics at 37 °C before starting the plasmid extraction.", "[Plasmid Extraction] Take out the Falcon tube with the cultured cells from the incubator.", "[Plasmid Extraction] Ce... |
63,826 | E-Gel™ 48-Well 2% Agarose Gels | 4 | null | https://www.protocols.io/view/e-gel-48-well-2-agarose-gels-cajsscne | Allyson Hirsch, George Testo | TITLE: E-Gel™ 48-Well 2% Agarose Gels
AUTHORS: Allyson Hirsch, George Testo
[DESCRIPTION]
E-Gel™48 Gels are pre-cast, ready-to-use, 48-well agarose gels designed for medium-throughput resolution of DNA fragments. Each gel contains 48 sample wells and 4 marker wells in a 2% high-resolution agarose. These types of st... | ["[Preparing Loading Plate(s)] DNA Away and Ethanol the workstation.", "[Preparing Loading Plate(s)] Thaw and spin down samples.", "[Preparing Loading Plate(s)] Add 13 µL of molecular grade water to the first 48 wells of a 96-well skirted plate.", "[Preparing Loading Plate(s)] Set multichannel pipette to 35 µL (more th... |
49,948 | Sewage sample extraction of total nucleic acid from secondary concentration pellet using a modified QIAamp Fast DNA Stool Mini Kit procedure | 1 | dx.doi.org/10.17504/protocols.io.buz4nx8w | https://www.protocols.io/view/sewage-sample-extraction-of-total-nucleic-acid-fro-buz4nx8w | Dilip Abraham, Venkata Raghava Mohan, gkang | TITLE: Sewage sample extraction of total nucleic acid from secondary concentration pellet using a modified QIAamp Fast DNA Stool Mini Kit procedure
AUTHORS: Dilip Abraham, Venkata Raghava Mohan, gkang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This procedure describes a modified extraction pro... | ["[Extraction of total nucleic acid from secondary concentration pellet using a modified QIAamp Fast DNA Stool Mini Kit procedure]\nMix InhibitEX Buffer thoroughly by shaking before use. If a precipitate has formed, Incubate at - for ~ or until all precipitate has fully dissolved.\n37 °C\n70 °C\nInhibitEX buffer is a l... |
59,223 | High Resolution "DIY" Photogrammetry - 'HRP' Protocol | 1 | dx.doi.org/10.17504/protocols.io.b53xq8pn | https://www.protocols.io/view/high-resolution-34-diy-34-photogrammetry-39-hrp-39-b53xq8pn | Yu Tang, Jacopo Niccolo Cerasoni, Emily Yuko Hallett | TITLE: High Resolution "DIY" Photogrammetry - 'HRP' Protocol
AUTHORS: Yu Tang, Jacopo Niccolo Cerasoni, Emily Yuko Hallett
[DESCRIPTION]
Photogrammetry is a method of calculating the three-dimensional shape of an object from a set of images. The advantages of Photogrammetry include the ability to reco... | ["[Setting Photographic Environment] Collect and prepare equipment.", "[Setting Photographic Environment] Set the camera on a tripod.", "[Setting Photographic Environment] Set the turntable on the table and set the items you want to scan on it, placing it as central as possible.", "[Setting Lighting Environment] If usi... |
76,920 | VU TIS Multimodal Molecular Imaging Pipeline for KPMP Biopsy Interrogation | 1 | null | https://www.protocols.click/view/vu-tis-multimodal-molecular-imaging-pipeline-for-k-cpcyvixw | Katerina V Djambazova, Lukasz Migas, Martin Dufresne, Jamie Allen, N. Heath Patterson, Léonore Tideman, Ellie Pingry, Madeline E. Colley, Angela R.S. Kruse, Melissa Farrow, Raf Van De Plas, Jeff Spraggins | TITLE: VU TIS Multimodal Molecular Imaging Pipeline for KPMP Biopsy Interrogation
AUTHORS: Katerina V Djambazova, Lukasz Migas, Martin Dufresne, Jamie Allen, N. Heath Patterson, Léonore Tideman, Ellie Pingry, Madeline E. Colley, Angela R.S. Kruse, Melissa Farrow, Raf Van De Plas, Jeff Spraggins
[DESCRIPTION]
This pro... | ["[Sample Interrogation Assays] Autofluorescence Microscopy (AF) is collected on all tissue sections prior to IMS\nAF QC Protocol: AFQC Protocol\nAF protocol: AF Microscopy", "[Sample Interrogation Assays] MALDI Imaging Mass Spectrometry (IMS)\nMatrix Deposition Protocol (Sublimation): Tissue Washing and Matrix deposit... |
92,902 | Whole-Genome Amplification of Respiratory Syncytial Virus (RSV) using Illumina CovidSeq reagents for Next-Generation Sequencing | 4 | dx.doi.org/10.17504/protocols.io.eq2lyjzbrlx9/v3 | https://www.protocols.io/view/whole-genome-amplification-of-respiratory-syncytia-c6yezfte | Carlos Davina-Nunez, Sonia Perez-Castro, Montse Godoy-Diz, Benito Regueiro-Garcia | TITLE: Whole-Genome Amplification of Respiratory Syncytial Virus (RSV) using Illumina CovidSeq reagents for Next-Generation Sequencing
AUTHORS: Carlos Davina-Nunez, Sonia Perez-Castro, Montse Godoy-Diz, Benito Regueiro-Garcia
[DESCRIPTION]
Protocol for amplification of RSV and for whole-genome sequencing. This protoco... | ["[Primer pools preparation] Pools WG: for samples of high viral load, covering the whole RSV genome.\n\nFor a final concentration of 10uM: add 607 ul of Nuclease-Free water to Pool 1 and 639 ul to Pool 2.\n \n \n \n\nPools GF: for samples of mid-to-low viral load, covering the G and F genes.\n\nFor a final concentrati... |
106,116 | Thawing Frozen Adherent Cell Lines | 4 | dx.doi.org/10.17504/protocols.io.bp2l6xz3klqe/v2 | https://www.protocols.io/view/thawing-frozen-adherent-cell-lines-djvc4n2w | Carolina Lopez | TITLE: Thawing Frozen Adherent Cell Lines
AUTHORS: Carolina Lopez
[DESCRIPTION]
This protocol describes the procedures from thawing and expanding adherent cell lines
[STEPS]
SECTION: Protocol
1. Day 1
Prepare media ahead of time and warm to room temperature
Spray down each bottle with 70% Ethanol before placing it in... | ["[Protocol] Day 1\nPrepare media ahead of time and warm to room temperature\nSpray down each bottle with 70% Ethanol before placing it into the TC hood\nPre-cool the centrifuge to 4ºC\nPrepare and label a 6-well plate, and aliquot 9 mL of TCM into a 15 mL conical for each tube of cells to be thawed\nFind the location ... |
106,622 | Mitochondrial subunit assay | 0 | dx.doi.org/10.17504/protocols.io.x54v92bmzl3e/v1 | https://www.protocols.io/view/mitochondrial-subunit-assay-dkc64sze | Isabel Lam, Alain Ndayisaba, Vikram Khurana | TITLE: Mitochondrial subunit assay
AUTHORS: Isabel Lam, Alain Ndayisaba, Vikram Khurana
[DESCRIPTION]
Mitochondrial subunit assay
[STEPS] | [] |
50,911 | THP-1 differentiation | 4 | null | https://www.protocols.io/view/thp-1-differentiation-bvx7n7rn | Juliane C Fernandes | TITLE: THP-1 differentiation
AUTHORS: Juliane C Fernandes
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Differentiation of THP-1 monocytic cell line in macrophage-like cells</div></div>
[STEPS]
?. [Plating and starting differentiation process]
Centrifuge at using
cultivated in RPMI 10% FBS Pen... | ["[Plating and starting differentiation process]\nCentrifuge at using\ncultivated in RPMI 10% FBS Pen/Strep in a humidified incubator at 5% CO2. Carefully check for any contamination before initiating the protocol.\nCentrifuge: 200 34, 8 min", "[Plating and starting differentiation process]\nEstimate the number of... |
20,573 | Food preference assay of C Elegans | null | dx.doi.org/10.17504/protocols.io.yb5fsq6 | null | Priota Islam | TITLE: Food preference assay of C Elegans
AUTHORS: Priota Islam
[STEPS]
?. [Preparing Bacterial solution of choice (Worm food)]
Fresh bacterial culture of OP50 and HB101 were prepared following the protocol Making OP50 solution from Frozen Stock
?. [Preparing worms]
Maintain N2s on NGM plates seeded with either OP50 o... | ["[Preparing Bacterial solution of choice (Worm food)]\nFresh bacterial culture of OP50 and HB101 were prepared following the protocol Making OP50 solution from Frozen Stock", "[Preparing worms]\nMaintain N2s on NGM plates seeded with either OP50 or HB101 or a mixture of both depending on experiment planChunk each set ... |
10,333 | 16S Metagenomic Sequencing Library Preparation (Modified version of Illumina) | 1 | dx.doi.org/10.17504/protocols.io.nb5daq6 | https://www.protocols.io/view/16s-metagenomic-sequencing-library-preparation-mod-nb5daq6 | Khine WT Wei | TITLE: 16S Metagenomic Sequencing Library Preparation (Modified version of Illumina)
AUTHORS: Khine WT Wei
[DESCRIPTION]
Metagenomic studies are commonly performed by analyzing the prokaryotic 16S ribosomal RNA (16S rRNA) gene. This protocol describes a workflow for preparing samples for sequencing the V3-V4 regions o... | [] |
19,927 | Nerve tissue processing for transmission electron microscopy (TEM) | 1 | dx.doi.org/10.17504/protocols.io.xpxfmpn | https://www.protocols.io/view/nerve-tissue-processing-for-transmission-electron-xpxfmpn | Natalia Biscola, Leif Havton | TITLE: Nerve tissue processing for transmission electron microscopy (TEM)
AUTHORS: Natalia Biscola, Leif Havton
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Transmission electron microscopy (TEM) studies promote an improved understanding of functional studies and provide critical ultrastruc... | ["[nerve tissue collection]\nAnimals are transcardially perfused with 0.12M Millonigs buffer (MB), ph=7.3, followed by 2% paraformaldehyde and 1.25% glutaraldehyde diluted in MB for", "[Dehydration]\nContinuing the dehydration place 100% propylene oxide in the tissues for", "[Fixation]\nFix tissues with 1% Osmium solut... |
55,204 | PRESTO-Tango Assay | 4 | null | https://www.protocols.io/view/presto-tango-assay-bz6cp9aw | Abigail Cornwell | TITLE: PRESTO-Tango Assay
AUTHORS: Abigail Cornwell
[DESCRIPTION]
PRESTO-Tango Assay protocol for assessing GPR68 activation by benzodiazepines at acidic pH.
[BEFORE_START]
Acidic media preparation (modified from Pera et al.): Rehydrate VWR Traceable pH/ORP meter (10539-802) in pH4.0 solution at least 30 minutes bef... | ["Day 1: Plated 400,000 HTLA cells/2mL of media in each well of a 6-well dish by bulk preparing 13mL media + 2.6x10^6 HTLA cells", "Day 2: Transfect 500ng GPR68-Tango (Addgene #66371) construct in 5 of the 6 wells using Lipofectamine 3000 (L3000008, Thermo Scientific) according to the Manufacturer's Instructions. Perfo... |
79,267 | XTT Assay for Detection of Bacterial Metabolic Activity in water-based Polyester Polyurethane | 1 | dx.doi.org/10.17504/protocols.io.4r3l27zbjg1y/v1 | https://www.protocols.io/view/xtt-assay-for-detection-of-bacterial-metabolic-act-crnbv5an | Nallely Magaña-Montiel, Luis F Muriel-Millán, Liliana Pardo-López | TITLE: XTT Assay for Detection of Bacterial Metabolic Activity in water-based Polyester Polyurethane
AUTHORS: Nallely Magaña-Montiel, Luis F Muriel-Millán, Liliana Pardo-López
[DESCRIPTION]
In microbial biodegradation assays, the detection of bacterial growth in water-based plastic dispersions can be difficult to mea... | ["[Culture media preparation] The strains' ability to grow using the commercial PU coating Impranil‱DLN as a carbon source is evaluated in Basal Medium, which is always supplemented with Instant Ocean Sea Salt (0.06 g•L-1).", "XTT solution\nPrepare a solution of at 2 mg•mL-1 in BM.", "[XTT experiment for detection o... |
85,917 | The Quantitative Loop-Mediated Isothermal Amplification Colorimetric-Phenol Red (QLAMP-PhR) Protocol | 4 | dx.doi.org/10.17504/protocols.io.3byl4qjkovo5/v1 | https://www.protocols.io/view/the-quantitative-loop-mediated-isothermal-amplific-cx55xq86 | abdulrahman.zuraik | TITLE: The Quantitative Loop-Mediated Isothermal Amplification Colorimetric-Phenol Red (QLAMP-PhR) Protocol
AUTHORS: abdulrahman.zuraik
[DESCRIPTION]
QLAMP-PhR Protocol
The LAMP technique was originally developed in 2000 by (Notomi, et al.).
In this proposed protocol, we aim to develop a new biomedical technique for... | ["Samples :\nstart with stool samples.\nThe acquired samples were stored in a freezer at −50 °C.", "DNA extraction :\nStool samples were removed from the freezer and kept at 37 °C for 20 min prior to use.\nGenomic DNA was extracted from the stool samples.\nAll DNA samples were stored at −50 °C until used.", "Primer des... |
null | null | null | dx.doi.org/10.17504/protocols.io.iyjcfun | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The method described here is from the PLoS ONE paper entitled "Joint time delay and Doppler passive acoustic 3D tracking, applied to studies of bats in natural habitats".<br />This method detects acoustic events (possible bat calls) and filters them according to their <br />c... | [] |
85,646 | KAPP-Sen TMC: Fixation of Cells and Nuclei for Chromium Fixed RNA Profiling | 1 | dx.doi.org/10.17504/protocols.io.x54v9py5zg3e/v1 | https://www.protocols.io/view/kapp-sen-tmc-fixation-of-cells-and-nuclei-for-chro-cxvnxn5e | Juliana Alcoforado Diniz, Dylan Baker, Jessica Garofalo, Paul Robson | TITLE: KAPP-Sen TMC: Fixation of Cells and Nuclei for Chromium Fixed RNA Profiling
AUTHORS: Juliana Alcoforado Diniz, Dylan Baker, Jessica Garofalo, Paul Robson
[DESCRIPTION]
Cells are fixated prior to scRNA-seq according to 10X Genomics protocol CG000478.
[STEPS]
SECTION: Fixation of Cells & Nuclei
1. Centrif... | ["[Fixation of Cells & Nuclei] Centrifuge sample at 350 rcf for 5 min at 4°C.", "[Fixation of Cells & Nuclei] Remove the supernatant without disturbing the pellet.", "[Fixation of Cells & Nuclei] Add 1 ml Fixation Buffer to the sample pellet and pipette mix 5x.", "[Fixation of Cells & Nuclei] Incubate f... |
43,625 | Rearing Bark and Ambrosia Beetles from Naturally Infested Wood | 3 | dx.doi.org/10.17504/protocols.io.bnuhmet6 | https://www.protocols.io/view/rearing-bark-and-ambrosia-beetles-from-naturally-i-bnuhmet6 | Jiri Hulcr, Andrew J. Johnson, Demian F Gomez | TITLE: Rearing Bark and Ambrosia Beetles from Naturally Infested Wood
AUTHORS: Jiri Hulcr, Andrew J. Johnson, Demian F Gomez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to rear bark and ambrosia beetles in naturally infested wood. </div><div class = "text-block"><span... | [] |
34,458 | Nuclei isolation from mouse lung for single nucleus RNASeq | null | dx.doi.org/10.17504/protocols.io.bdv2i68e | null | Jeffrey Koenitzer, Ben Humphreys | TITLE: Nuclei isolation from mouse lung for single nucleus RNASeq
AUTHORS: Jeffrey Koenitzer, Ben Humphreys
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is for</span><span style = "font-weight:bold;"> nuclei isolation from mouse lung for single nucleus RNASeq</span><span style... | ["Pre-cool all instruments (including centrifuges), buffers, and tubes.\nNote: All steps are performed or in cold room ( ) to minimize RNA degradation.", "Remove mouse lung sample from -80 ºC freezer and trim a ~6 mm3 piece.", "Transfer the minced tissue and buffer to a GentleMacs C tube.", "Run m_lung_01 program and... |
null | null | null | dx.doi.org/10.17504/protocols.io.hweb7be | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>T cell dependent cytotoxicity assay for measuring bispecific T cell engager (BiTE<strong>®)</strong> activity.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
75,154 | Salmonella Quick Electroporation Protocol | 1 | dx.doi.org/10.17504/protocols.io.261ge3wxwl47/v1 | https://www.protocols.io/view/salmonella-quick-electroporation-protocol-cmmsu46e | Christina M. Ferreira, Jie Zheng, Rebeccabell | TITLE: Salmonella Quick Electroporation Protocol
AUTHORS: Christina M. Ferreira, Jie Zheng, Rebeccabell
[DESCRIPTION]
Protocol for generating electrocompetent Salmonella cells and transforming them in less than 1-day, with a high transformation efficiency.
[BEFORE_START]
Be sure to have your intended material (plasm... | ["[Day 3A: Preparation of Electrocompetent Cells] In a 125mL Erlenmeyer flask containing 25mL of fresh TSB, transfer 1mL of the overnight culture (1:25 dilution) and incubate at 35°C±2°C, without shaking for 3 hours.", "[Day 3A: Preparation of Electrocompetent Cells] Before the end of the incubation, pre-warm SOC (meas... |
83,018 | A Pilot Study For Developing an Adolescent Smoking Cessation Program Based on Emotional and Motivational Factors | 1 | dx.doi.org/10.17504/protocols.io.36wgq3r45lk5/v1 | https://www.protocols.click/view/a-pilot-study-for-developing-an-adolescent-smoking-cvbiw2ke | Mohammad Eko Fitrianto, Basu Swastha Dharmmesta, Bernardinus Maria Purwanto | TITLE: A Pilot Study For Developing an Adolescent Smoking Cessation Program Based on Emotional and Motivational Factors
AUTHORS: Mohammad Eko Fitrianto, Basu Swastha Dharmmesta, Bernardinus Maria Purwanto
[DESCRIPTION]
This pilot study aims to explore the effect of emotional and motivational factors on peer support in... | ["[Preparation] Request ethical approval for your study", "[Preparation] Approach several high schools to obtain a willingness to participate (allowed their students participation).", "[Data collection] Before the data collection is started. Ask the homeroom teacher's willingness to distribute questionnaires to their s... |
85,450 | Utilisation de l'ordinateur 'slaker' pour réaliser des QuantiSlakeTests (QST) | 1 | dx.doi.org/10.17504/protocols.io.rm7vzxyk5gx1/v1 | https://www.protocols.click/view/utilisation-de-l-39-ordinateur-39-slaker-39-pour-r-cxpixmke | f.vanwindekens | TITLE: Utilisation de l'ordinateur 'slaker' pour réaliser des QuantiSlakeTests (QST)
AUTHORS: f.vanwindekens
[DESCRIPTION]
slaking lab draft protocol in french
[STEPS]
1. Version 3.0 !
2. Allumer l’ordinateur
USER: slaker
PASSWORD: *
3. Lancer le programme
Dans le terminal (fênetre blanche ou no... | ["Version 3.0 !", "Allumer l’ordinateur\n\n\n\nUSER: slaker\n\n\nPASSWORD: *", "Lancer le programme\n\n\n\nDans le terminal (fênetre blanche ou noire qui s’ouvre automatiquement, ou cliquer sur l’icône Xterm), taper: \nAppSlake\n (on obtient donc \n[slaker@kingkong ~]$ AppSlake\n ) et appuyer sur enter.\n\n\nUne fenêtr... |
95,134 | Passaging and Seeding Mouse Embryonic Fibroblasts (MEFs) for Experiments | 1 | dx.doi.org/10.17504/protocols.io.6qpvr3jdbvmk/v1 | https://www.protocols.io/view/passaging-and-seeding-mouse-embryonic-fibroblasts-c856zy9e | madalynn.erb | TITLE: Passaging and Seeding Mouse Embryonic Fibroblasts (MEFs) for Experiments
AUTHORS: madalynn.erb
[DESCRIPTION]
This protocol details the passaging and seeding mouse embryonic fibroblasts (MEFs) for experiments.
[STEPS]
SECTION: Passaging and Seeding Mouse Embryonic Fibroblasts (MEFs) for Experiments
1. Passage c... | ["[Passaging and Seeding Mouse Embryonic Fibroblasts (MEFs) for Experiments] Passage cells when confluency exceeds 60%.", "[Passaging and Seeding Mouse Embryonic Fibroblasts (MEFs) for Experiments] Remove media.", "[Passaging and Seeding Mouse Embryonic Fibroblasts (MEFs) for Experiments] Wash cells with 5 mL prewarmed... |
56,525 | In vitro synthesis of PE2 (nCas9-MMLV RT fusion) polyA mRNA using T7 RNA polymerase | 4 | dx.doi.org/10.17504/protocols.io.b3fmqjk6 | https://www.protocols.io/view/in-vitro-synthesis-of-pe2-ncas9-mmlv-rt-fusion-pol-b3fmqjk6 | Donald Rio | TITLE: In vitro synthesis of PE2 (nCas9-MMLV RT fusion) polyA mRNA using T7 RNA polymerase
AUTHORS: Donald Rio
[DESCRIPTION]
We describe the preparation of synthetic capped and polyadenylated messenger RNA (mRNA) encoding a Cas9 nickase-reverse transcriptase fusion protein (PE2) for use in genome editing with a metho... | ["[Protocol Overview] Preparation of linearized plasmid DNA encoding the PE2 protein for use as a template for in vitro transcription by T7 RNA polymerase.", "[Protocol Overview] Synthesis of mRNA by T7 RNA polymerase, using a 5’ cap nucleotide to initiate the mRNA and using E. coli poly A polymerase to add a synthetic... |
71,694 | ALS Mouse Tissue Processing | 4 | null | https://www.protocols.io/view/als-mouse-tissue-processing-ch9nt95e | katesama | TITLE: ALS Mouse Tissue Processing
AUTHORS: katesama
[DESCRIPTION]
This protocol describes how to prepare tissues and blood for downstream applications after the ALS mouse study.
[STEPS]
SECTION: Blood & Plasma
1. Blood and Plasma Processing
SECTION: Blood & Plasma
1.1. After cardiac puncture and blood collec... | ["[Blood & Plasma] Blood and Plasma Processing", "[Blood & Plasma] After cardiac puncture and blood collection in K3-EDTA tubes, invert the tube a few times to ensure mixing with EDTA coating and keep it at RT until centrifugation within 4 hours of collection.", "[Blood & Plasma] Spin whole blood at 1,600xg... |
43,878 | Sensitivity and specificity test of toehold | 1 | null | https://www.protocols.io/view/sensitivity-and-specificity-test-of-toehold-bn4emgte | Hung Liang Pai, Cheng-Ruei Yang | TITLE: Sensitivity and specificity test of toehold
AUTHORS: Hung Liang Pai, Cheng-Ruei Yang
[STEPS]
?. [Preparation]
Sterilize the bench, and put on a labmat
?. [Preparation]
Thaw the reagents including 1. DNase/ RNase free water (store in -20°C) 2. solution A (store in -80°C) 3. solution B (store in -80°C) 4. RNase i... | ["[Preparation]\nSterilize the bench, and put on a labmat", "[Preparation]\nThaw the reagents including 1. DNase/ RNase free water (store in -20°C) 2. solution A (store in -80°C) 3. solution B (store in -80°C) 4. RNase inhibitor (store in -20°C) 5.toehold switches with invertase DNA (store in 4°C) 6.miRNA as the trigge... |
49,934 | Bacterial abundance from grass litter - Flow cytometry | 4 | dx.doi.org/10.17504/protocols.io.buznnx5e | https://www.protocols.io/view/bacterial-abundance-from-grass-litter-flow-cytomet-buznnx5e | cweihe | TITLE: Bacterial abundance from grass litter - Flow cytometry
AUTHORS: cweihe
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used to get the abundance of bacteria via flow cytometry from ground, decomposing grass leaf litter. </div></div>
[STEPS]
?. Add of Pi-buffered GTA soluti... | ["Add of Pi-buffered GTA solution to ground grass litter sample in a 50 ml tube.\n5000 µl\n0.1 g", "store fixed sample in the dark at for up to 30 days\n4 °C", "When you are ready to run your samples on the flow cytometer add of 0.1M TSP buffer and vortex.\n550 µl", "Put samples from step 3 in ultrasonic bath at f... |
40,329 | TAP media preparation | 4 | null | https://www.protocols.io/view/tap-media-preparation-bjmhkk36 | Joao Vitor Molino | TITLE: TAP media preparation
AUTHORS: Joao Vitor Molino
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes the preparation of TAP media. Usually used for growing algae cells, as Chlamydomonas reinhardtii. The protocol is derived from the protocol descrived at </span><a hre... | ["[Components mixing]\nAdd approximatelly of ddH20 to a large enough vessel. Add a magnetic bar and start and keep mixing with a magnetic stirrer during the preparation. Place pH probe electrode in the solution for pH monitoringFor Add Add Add Add Add , then add drops until is reachedStop mixing, and a... |
79,753 | Schistosoma mansoni cercariae transformation (without needle) | 4 | dx.doi.org/10.17504/protocols.io.8epv5jp36l1b/v1 | https://www.protocols.io/view/schistosoma-mansoni-cercariae-transformation-witho-cr5hv836 | Sarah K Buddenborg | TITLE: Schistosoma mansoni cercariae transformation (without needle)
AUTHORS: Sarah K Buddenborg
[DESCRIPTION]
Free-living aquatic S. mansoni cercariae transform into the first intramammalian stage, called schistosomula or somules, by burrowing in the host skin. Upon contact, cercariae begin to enter the skin and lose... | ["[Cercariae collection] Shed cercariae from snails in a 6-well plate (see protocol \"Schistosoma mansoni cercariae shedding\"). The snails can be shed for up to 2 hrs by collecting cercariae and replacing with fresh water every 30 min", "Using a sterile transfer pipette, dispense cercariae into sterile 15ml falcon tub... |
45,312 | Induced Neurons for the Study of Neurodegenerative and Neurodevelopmental Disorders | 2 | dx.doi.org/10.17504/protocols.io.bqg8mtzw | https://www.protocols.io/view/induced-neurons-for-the-study-of-neurodegenerative-bqg8mtzw | Evelyn J. Sauter, Lisa K. Kutsche, Simon D. Klapper, Volker Busskamp | TITLE: Induced Neurons for the Study of Neurodegenerative and Neurodevelopmental Disorders
AUTHORS: Evelyn J. Sauter, Lisa K. Kutsche, Simon D. Klapper, Volker Busskamp
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Patient-derived or genomically modified human induced pluripotent stem cells (iPSCs... | [] |
104,076 | OT-2 Custom Mixing with Single or Multi-Channel Pipette | 0 | dx.doi.org/10.17504/protocols.io.5jyl82686l2w/v1 | https://www.protocols.io/view/ot-2-custom-mixing-with-single-or-multi-channel-pi-dhvk364w | Ángel Goñi-Moreno, Ana Mariya Anhel, Paula Mugica-Galan | TITLE: OT-2 Custom Mixing with Single or Multi-Channel Pipette
AUTHORS: Ángel Goñi-Moreno, Ana Mariya Anhel, Paula Mugica-Galan
[DESCRIPTION]
This protocol is created to help efficiently produce high-throughput plates with different reagents using either a single or multi-channel pipette controlled by an Opentrons OT-... | ["[Files Preparation] Preparing Customized Template\n\nPreparing the template (a .xlsx) with the specific variables for each experiment.\n\nAttached is a template of the variable file with several sheets and a PDF file explaining each variable:\nGeneralVariables: These are variables mainly related to the labware to be ... |
null | null | null | dx.doi.org/10.17504/protocols.io.pvvdn66 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A chronic illness in childhood has a negative impact on the paediatric patient and on family functioning. Psychological stress in parents influences the level of adjustment to the illness of their children. The Pediatric Inventory for Parents (PIP) was designed to measure str... | [] |
95,704 | Extract-N-Amp Equivalent DNA Extraction Protocol | 0 | dx.doi.org/10.17504/protocols.io.5jyl8p458g2w/v1 | https://www.protocols.io/view/extract-n-amp-equivalent-dna-extraction-protocol-c9pyz5pw | Stephen Douglas Russell | TITLE: Extract-N-Amp Equivalent DNA Extraction Protocol
AUTHORS: Stephen Douglas Russell
[DESCRIPTION]
This extraction protocol uses an Extract-N-Amp equivalent solution to quickly and cheaply perform DNA extractions. This protocol has been widely used for dried specimens of macrofungi, but will work for other organis... | ["[Create the Extraction Solution] Add 10mL of 1 M Tris stock into a 100mL Erlenmeyer flask. \n\nFor larger batches:\n50mL for 500mL of end product in a 500mL flask.\n1000mL for 1000mL of end product in a 1000mL flask.", "[Create the Extraction Solution] Add 1.86g of KCl.\n\nFor larger batches:\n9.3g for 500mL of end p... |
93,563 | Assembling simple and universal adjustable multiheight smartphone stand for lab microscopes | 1 | dx.doi.org/10.17504/protocols.io.n2bvj3m2plk5/v1 | https://www.protocols.io/view/assembling-simple-and-universal-adjustable-multihe-c7k3zkyn | Haruka Honda, Noritaka Miyamoto, Hisayuki Miyajima, Keigo Yoshida, Yuichi Tanaka | TITLE: Assembling simple and universal adjustable multiheight smartphone stand for lab microscopes
AUTHORS: Haruka Honda, Noritaka Miyamoto, Hisayuki Miyajima, Keigo Yoshida, Yuichi Tanaka
[DESCRIPTION]
Cameras in mobile devices such as smartphones and tablets have recently been used to capture or display images from ... | ["[Fabricating the upper stage] An upper stage is built using an aluminum plate (70 mm × 40 mm × 3 mm), 20 mm × 20 mm T-slot aluminum extrusion (length is 115 mm), two T-slot nuts, and two countersunk screws.\nAs in the figure below two holes are drilled into the aluminum plate using a drill.", "[Fabricating the upper ... |
57,811 | Preparing feeder-free hPSCs for nucleofection | 4 | dx.doi.org/10.17504/protocols.io.b4ptqvnn | https://www.protocols.io/view/preparing-feeder-free-hpscs-for-nucleofection-b4ptqvnn | Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner | TITLE: Preparing feeder-free hPSCs for nucleofection
AUTHORS: Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner
[DESCRIPTION]
This protocol describes the standard procedure preparing feeder-free human pluripotent stem cells (hPSCs) for nucleofection.
General notes
1. Throughout this protocol, ... | ["Cells are ready for nucleofection when the culture reaches 70-80% confluency\n\nFor a detailed protocol on growing feeder-free hPSCs, refer to the collection \"Feeder-free culturing of hPSCs;\" dx.doi.org/10.17504/protocols.io.b4mcqu2w", "Coat 6-well plates with VTN/Matrigel/Geltrex as depicted in the collection “Fee... |
null | null | null | dx.doi.org/10.17504/protocols.io.e7wbhpe | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.iy3cfyn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
41,880 | Restriction Digest -- CHEM 584 | 1 | dx.doi.org/10.17504/protocols.io.bk5yky7w | https://www.protocols.io/view/restriction-digest-chem-584-bk5yky7w | New England Biolabs, Ken Christensen | TITLE: Restriction Digest -- CHEM 584
AUTHORS: New England Biolabs, Ken Christensen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The following is a "typical" restriction endonuclease reaction. Please see the "guidelines" tab below for the NEB tips on optimizing restriction digests.</div></div>
[... | ["Set up the following reaction (total reaction volume 50µl). AB1Restriction Enzyme10 units is sufficient, generally 1µl is used2DNA1 µg310X CutSmart Buffer5 µl (1X)4Total Reaction Volume50 µl5Incubation Time1 hour*6Incubation TemperatureEnzyme dependent* Can be decreased to 5-15 minutes by using a Time-Saver™ Qualifi... |
97,092 | USDA LTAR Common Experiment measurement: Depth to water table | 0 | dx.doi.org/10.17504/protocols.io.kqdg32eb7v25/v1 | https://www.protocols.io/view/usda-ltar-common-experiment-measurement-depth-to-w-da3c2giw | Keirith A. Snyder, Amartya Saha | TITLE: USDA LTAR Common Experiment measurement: Depth to water table
AUTHORS: Keirith A. Snyder, Amartya Saha
[DESCRIPTION]
Groundwater is water held beneath the land surface in rock and soil pore space. The upper surface of this saturated water zone is called the water table. Depth to groundwater, also referred to as... | ["[Data processing and quality control] Recommendations on data processing and quality control follow the general recommendations for water quantity variables. Please refer to the Quality Control section in the USDA LTAR Common Experiment measurement: Best practices for collection, handling, and analyses of water quant... |
45,492 | Preparation of Enhanced Orthogonal Aminoacyl-tRNA-Synthetase | 1 | dx.doi.org/10.17504/protocols.io.bqnumvew | https://www.protocols.io/view/preparation-of-enhanced-orthogonal-aminoacyl-trna-bqnumvew | Anne Zemella, Theresa Richter, Lena Thoring, Stefan Kubick | TITLE: Preparation of Enhanced Orthogonal Aminoacyl-tRNA-Synthetase
AUTHORS: Anne Zemella, Theresa Richter, Lena Thoring, Stefan Kubick
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">This is part 3.1 of the "A Combined Cell-Free Protein Synthesis and Fluorescence-B... | ["[3.1 Preparation of Enhanced Orthogonal Aminoacyl-tRNA-Synthetase]\nFor prokaryotic cell-free synthesis, the eAzFRS gene should be cloned into a vector containing a T7 promotor, ribosomal binding site, and T7 terminator such as pIX3.0, pIVEX2.3d, and pIVEX2.4d vectors or alternatively containing a T5 promotor such as... |
104,066 | Singleplex Assay for Function Measurements | 0 | dx.doi.org/10.17504/protocols.io.dm6gpzwx8lzp/v2 | https://www.protocols.io/view/singleplex-assay-for-function-measurements-dhva362e | David Ross | TITLE: Singleplex Assay for Function Measurements
AUTHORS: David Ross
[DESCRIPTION]
This protocol outlines an assay for measuring the function of plasmid variants in singleplex.
The inputs include separate E. coli glycerol stocks for each variant. The protocol begins with several growths which convert the separate g... | ["[Culture Preparation] For each variant to be tested, fill a 15 mL snap-cap culture tube with 5 mL of M9 media.\nUse a scraping from the glycerol stock for each clonal variant and place into its culture tube.", "[Prepare the automation system or liquid handler] Load required reagents (M9 media, additives, PBS, etc.) a... |
106,625 | Western blot of amplified fibrils after Proteinase K digestion | 0 | dx.doi.org/10.17504/protocols.io.j8nlk81e1l5r/v1 | https://www.protocols.io/view/western-blot-of-amplified-fibrils-after-proteinase-dkc94sz6 | Isabel Lam, Alain Ndayisaba, Vikram Khurana | TITLE: Western blot of amplified fibrils after Proteinase K digestion
AUTHORS: Isabel Lam, Alain Ndayisaba, Vikram Khurana
[DESCRIPTION]
Western blot of amplified fibrils after Proteinase K digestion
[STEPS]
1. | [] |
96,852 | PROTOCOL for “Systemic inflammation triggers long-lasting neuroinflammation and accelerates neurodegeneration in a rat model of Parkinson’s disease overexpressing human α-synuclein” | 2 | dx.doi.org/10.17504/protocols.io.j8nlkoj65v5r/v2 | https://www.protocols.io/view/protocol-for-systemic-inflammation-triggers-long-l-datu2enw | mariangela.massarocenere, Valerio Chiurchiù, Nicola Biagio Mercuri | TITLE: PROTOCOL for “Systemic inflammation triggers long-lasting neuroinflammation and accelerates neurodegeneration in a rat model of Parkinson’s disease overexpressing human α-synuclein”
AUTHORS: mariangela.massarocenere, Valerio Chiurchiù, Nicola Biagio Mercuri
[DESCRIPTION]
Methodological collection for characteri... | [] |
43,833 | TaqMan qPCR assay for detecting Batrachochytrium dendrobatidis (Bd) | 4 | dx.doi.org/10.17504/protocols.io.bn2zmgf6 | https://www.protocols.io/view/taqman-qpcr-assay-for-detecting-batrachochytrium-d-bn2zmgf6 | Omneya Ahmed Osman, Mats Töpel, Tomas Larsson, Alexander Eiler | TITLE: TaqMan qPCR assay for detecting Batrachochytrium dendrobatidis (Bd)
AUTHORS: Omneya Ahmed Osman, Mats Töpel, Tomas Larsson, Alexander Eiler
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The fungus Batrachochytrium dendrobatidis (Bd) was first detected in Norway in 2017, and thus indicate th... | ["[DNA extraction]\nDNA extraction was performed using Qiagen DNeasy power water sterivex kit. The quality of the extracted DNA was estimated using Nanodrop. Qiagen DNeasy power water sterivex kit: https://www.qiagen.com/se/resources/resourcedetail?id=c5fe7d5f-070a-4ebe-ac04-4bbf05a13e91&lang=en", "[Real time PCR]\nA... |
65,652 | OMS Atlas FFPE Spatial Mapping | 1 | null | https://www.protocols.io/view/oms-atlas-ffpe-spatial-mapping-cccussww | Brett Johnson, Danielle Galipeau, George Thomas | TITLE: OMS Atlas FFPE Spatial Mapping
AUTHORS: Brett Johnson, Danielle Galipeau, George Thomas
[DESCRIPTION]
This protocol describes the procedure by which the OMS Atlas serially sections a FFPE block, prepares the resulting slides, and then distributes the specimens for downstream analysis.
[BEFORE_START]
Trans... | ["[Preparation] Verify the identity of the FFPE block to be cut against written request for sectioning.", "[Preparation] Label all slides with a unique BEMS ID and slide number, corresponding to the written request and FFPE spatial map (below).", "[Sectioning] Align block on microtome to minimize tissue loss.", "[Secti... |
103,799 | How to Improve the Reliability of qPCR Detection with Target Gene-optimized Internal Standards | 0 | dx.doi.org/10.17504/protocols.io.14egn6e7pl5d/v1 | https://www.protocols.io/view/how-to-improve-the-reliability-of-qpcr-detection-w-dhkx34xn | Jonathan Phillips, Gregor Blaha | TITLE: How to Improve the Reliability of qPCR Detection with Target Gene-optimized Internal Standards
AUTHORS: Jonathan Phillips, Gregor Blaha
[DESCRIPTION]
Achieving robust qPCR results requires both sensitive and accurate detection of target genes. This is particularly challenging for pathogen detection in field sam... | [] |
102,989 | Shipping live Daphnia | 0 | null | https://www.protocols.io/view/shipping-live-daphnia-dgtm3wk6 | Molly Fredericks, Jeff Dudycha, Carla Caceres, Matt Bruner | TITLE: Shipping live Daphnia
AUTHORS: Molly Fredericks, Jeff Dudycha, Carla Caceres, Matt Bruner
[DESCRIPTION]
Background:
Daphnia are small zooplankton oft... | ["Label 50mL conical/falcon tubes with the species, genotype, and date in which the Daphnia were placed into the tubes.", "Fill up the 50mL conical/falcon tubes with 45ml of filtered lake water or Artificial Daphnia Media (ADaM). Other Daphnia media, such as COMBO, may work.", "Place up to 6 individuals per tube.", "Fe... |
90,591 | Protocol to isolate and fix nuclei from cryopreserved left cortex mouse bridge samples for IGVF | 4 | null | https://www.protocols.io/view/protocol-to-isolate-and-fix-nuclei-from-cryopreser-c4p7yvrn | Elisabeth Rebboah | TITLE: Protocol to isolate and fix nuclei from cryopreserved left cortex mouse bridge samples for IGVF
AUTHORS: Elisabeth Rebboah
[DESCRIPTION]
This protocol describes isolation of nuclei from 10 week old mouse left cerebral cortex from B6J and CASTJ, preparation of a single nucleus suspension, and fixation for single... | ["[Setup] Label tubes.", "[Setup] Pre-chill centrifuge to 4C.", "[Setup] Prepare ice buckets.", "[Setup] Prepare 35 ml lysis buffer on ice in a 50 mL conical tube. Distribute 2 mL into 8 gentleMACS C Tubes on ice. Add 175 ul RNase inhibitor to the lysis buffer aliquot the day of the experiment.", "[Setup] Prepare 3.5 m... |
50,171 | Pristionchus Whole Genome Sequence Analysis | 5 | null | https://www.protocols.io/view/pristionchus-whole-genome-sequence-analysis-bu83nzyn | erick.rios. , Ray Hong | TITLE: Pristionchus Whole Genome Sequence Analysis
AUTHORS: erick.rios. , Ray Hong
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>With whole genome sequencing becoming more affordable and accessible every year, more diverse research groups will be capable of overcoming barriers to entry to ut... | ["[Preparing the read files]\nCreate a workspace folder and download the sequence files in the compressed format, fq.gz. Each genome should be at least two files from paired-end reads. BGI files may need to be concatenated into two files. Each compressed genome file could be up to 1 Gb.", "[Preparing the read files]\nD... |
65,238 | ProDentim(#1 Teeth Pills) Better Smile Or Another Scam? | 3 | dx.doi.org/10.17504/protocols.io.e6nvwknddvmk/v1 | https://www.protocols.io/view/prodentim-1-teeth-pills-better-smile-or-another-sc-cbxwsppe | prodentim | TITLE: ProDentim(#1 Teeth Pills) Better Smile Or Another Scam?
AUTHORS: prodentim
[DESCRIPTION]
The ProDentim is a natural dietary supplement that supports healthy gums and strong teeth as well as provides a safe and all-natural treatment for a variety of dental conditions. ProDentim pill produces calming effects by... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.ntydepw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Files:</p>
<p>1 administration protocol</p>
<p>2-5 scoring forms (versions 1A, 1B, 2A, 2B)</p>
<p> </p>
<p>For communication regarding (partial) translation of the files please contact the authors.</p>
[STEPS] | [] |
28,427 | Virus | null | dx.doi.org/10.17504/protocols.io.7zjhp4n | null | Norfitriah Mohamed Sohaimi, Mohd Hair Bejo, Abdul Rahman Omar, Aini Ideris, Nurulfiza Mat Isa | TITLE: Virus
AUTHORS: Norfitriah Mohamed Sohaimi, Mohd Hair Bejo, Abdul Rahman Omar, Aini Ideris, Nurulfiza Mat Isa
[STEPS] | [] |
97,508 | CODA (part 2): calculate registration on low-resolution tissue images | HuBMAP | JHU-TMC | 0 | dx.doi.org/10.17504/protocols.io.kxygxym3dl8j/v1 | https://www.protocols.io/view/coda-part-2-calculate-registration-on-low-resoluti-dbgc2jsw | Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Ashley Kiemen, Sashank Reddy, Denis Wirtz | TITLE: CODA (part 2): calculate registration on low-resolution tissue images | HuBMAP | JHU-TMC
AUTHORS: Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Ashley Kiemen, Sashank Reddy, Denis Wirtz
[DESCRIPTION]
CODA workflow part 2. Calculate registration on low-resolution tissue images
[STEPS]
SECTION: Calculating the tissu... | ["[Calculating the tissue space] For most images, a resolution of 1x should be sufficient. If the 1x results are not well registered, or registration of small tissues (such as needle biopsies) is desired, try calculating registration at a higher resolution such as 2x or 4x.", "[Calculating the tissue space] The quality... |
72,463 | Factors influencing COVID-19 vaccine acceptance and hesitancy among
pharmacy students in Bangladesh: a cross sectional study | 1 | dx.doi.org/10.17504/protocols.io.n2bvj88wngk5/v1 | https://www.protocols.io/view/factors-influencing-covid-19-vaccine-acceptance-an-cizpuf5n | Md. Mohabbot Hossen | TITLE: Factors influencing COVID-19 vaccine acceptance and hesitancy among
pharmacy students in Bangladesh: a cross sectional study
AUTHORS: Md. Mohabbot Hossen
[DESCRIPTION]
To assess different factors influencing COVID-19 vaccine acceptance and hesitancy among pharmacy students in Bangladesh an anonymous self-admin... | ["1. Study design", "An anonymous self-administered questionnaire was deployed online using Google form.", "2. Settings and participants", "Data were collected between 15th October, 2021 and 15th December, 2021.", "Currently pharmacy students are studying at public or private university in Bangladesh.", "Online link wa... |
null | null | null | dx.doi.org/10.17504/protocols.io.e9ebh3e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><span style="color: #000000; font-family: 'Open Sans', sans-serif; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 16px; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space:... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.m2kc8cw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?. | [] |
69,915 | Developments in PGC Mindanao Bioinformatics Digital Infrastructure | 1 | null | https://www.protocols.io/view/developments-in-pgc-mindanao-bioinformatics-digita-cgh3tt8n | Paul Lorenzo A Gaite, Dr Ritchie Mae T Gamot | TITLE: Developments in PGC Mindanao Bioinformatics Digital Infrastructure
AUTHORS: Paul Lorenzo A Gaite, Dr Ritchie Mae T Gamot
[DESCRIPTION]
One of the major challenges that was identified for bioinformatics in PGC Mindanao was its underdeveloped digital infrastructure. Fortunately, there was an ample portion from th... | ["Structured cabling of Sequencing and Bioinformatics laboratories\n\nThis section shows the structured cabling of the sequencing and bioinformatics laboratories. \n\nFigure 1 shows the cabling that connects the sequencing and bioinformatics laboratories to the university's internet system via one of the internet se... |
27,466 | UC Davis - Glucagon | null | dx.doi.org/10.17504/protocols.io.63ihgke | null | Peter Havel | TITLE: UC Davis - Glucagon
AUTHORS: Peter Havel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Glucagon is a 29 amino acid polypeptide processed from proglucagon in pancreatic alpha cells. In intestinal L-cells proglu... | ["Prepare enzyme conjugate 1X solution and wash buffer 1X solution.", "Prepare sufficient microplate wells to accommodate Calibrators, controls and samples in duplicate.", "Pipette 10 µL each of Calibrators, controls and samples into appropriate wells.", "Add 50 µL enzyme conjugate 1X solution to each well and attach t... |
67,445 | https://www.facebook.com/PrimaWeightLossDragonsDenUK/ | 1 | dx.doi.org/10.17504/protocols.io.ewov1np8ogr2/v1 | https://www.protocols.io/view/https-www-facebook-com-primaweightlossdragonsdenuk-cd4vs8w6 | alexballosz | TITLE: https://www.facebook.com/PrimaWeightLossDragonsDenUK/
AUTHORS: alexballosz
[DESCRIPTION]
Prima Weight Loss Dragons Den UK
Prima Weight Loss Dragons Den UK is a company that helps people who are interested in using their fitness knowledge to make more money. They offer an online blog and video courses, which p... | ["[https://www.facebook.com/PrimaWeightLossDragonsDenUK/]"] |
82,919 | Microscopy-based GSH bead protein-protein interaction assay | 4 | dx.doi.org/10.17504/protocols.io.4r3l27xdxg1y/v1 | https://www.protocols.io/view/microscopy-based-gsh-bead-protein-protein-interact-cu8fwztn | Minghao Chen, Xuefeng Ren | TITLE: Microscopy-based GSH bead protein-protein interaction assay
AUTHORS: Minghao Chen, Xuefeng Ren
[DESCRIPTION]
Microscopy-based GSH bead protein-protein interaction assay
[STEPS]
1. Wash pre-blocked glutathione sepharose beads (GE Healthcare) with the reaction buffer (25 mM HEPES at pH 7.5, 150 mM NaCl, 1 mM MgC... | ["Wash pre-blocked glutathione sepharose beads (GE Healthcare) with the reaction buffer (25 mM HEPES at pH 7.5, 150 mM NaCl, 1 mM MgCl2 and 1 mM TCEP) three times.", "Make a mixture of 1 μM purified GST tagged protein and 500 nM purified fluorescent protein in total 70 μl", "Incubate at Room temperature for 30 min, sam... |
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