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 |
|---|---|---|---|---|---|---|---|
100,171 | MP Biomedicals FastDNA™ SPIN Kit | 0 | null | https://www.protocols.io/view/mp-biomedicals-fastdna-spin-kit-dd3j28kn | Karen Keegan | TITLE: MP Biomedicals FastDNA™ SPIN Kit
AUTHORS: Karen Keegan
[DESCRIPTION]
MP Biomedicals FastDNA‱
SPIN Kit for feces
[STEPS]
SECTION: MP Biomedicals FastDNA™ SPIN Kit for feces
1. In a 2 mL Lysing Matrix E tube, add 500 mg feces sample, 825 μL Sodium
Phosphate Buffer, and 275 μL of PLS solution. Shake to mix. Vorte... | ["[MP Biomedicals FastDNA™ SPIN Kit for feces] In a 2 mL Lysing Matrix E tube, add 500 mg feces sample, 825 μL Sodium\nPhosphate Buffer, and 275 μL of PLS solution. Shake to mix. Vortex 10-15\nseconds.", "[MP Biomedicals FastDNA™ SPIN Kit for feces] Centrifuge samples at 14,000 x g for 5 minutes and decant supernatant.... |
29,507 | Flow-cytometry-based in vitro assay for assessing T-cell-mediated cytotoxicity against a target cell line (24-well plate, pmel-1 or OT-I T cells, MC38 cell line) | null | dx.doi.org/10.17504/protocols.io.83bhyin | null | Bulent Arman Aksoy, Pinar Aksoy, Elinor Gottschalk, Jeff Hammerbacher | TITLE: Flow-cytometry-based in vitro assay for assessing T-cell-mediated cytotoxicity against a target cell line (24-well plate, pmel-1 or OT-I T cells, MC38 cell line)
AUTHORS: Bulent Arman Aksoy, Pinar Aksoy, Elinor Gottschalk, Jeff Hammerbacher
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">In v... | ["[Day 0 - Seeding the target cells]\nCollect at least 3 million MC38s by trypsinizing them from an on-going culture", "[Day 0 - Seeding the target cells]\nSpin them down at for at and re-suspend them in fresh media at a 250,000 cells per mL concentration\nCentrifuge: 200 34\n4 °C", "[Day 0 - Seeding the target cell... |
77,502 | Characterization of the VKORC1 and CYP2C9 genotypes | 1 | dx.doi.org/10.17504/protocols.io.kxygx9edzg8j/v2 | https://www.protocols.io/view/characterization-of-the-vkorc1-and-cyp2c9-genotype-cpw6vphe | Mirsada Causevic, Edin Begic | TITLE: Characterization of the VKORC1 and CYP2C9 genotypes
AUTHORS: Mirsada Causevic, Edin Begic
[DESCRIPTION]
Vitamin K antagonists are anticoagulants which represent widely prescribed drugs for prevention and treatment of thromboembolic disorders.
The molecular target of these drugs is vitamin K epoxide reductase ... | ["[Genomic DNA extraction] Patients' whole blood was collected in ethylenediaminetetraacetic acid (EDTA)-containing tubes and stored at -20°C until use. Genomic DNA extraction from the human whole blood, that is, leukocytes, was carried out according to the protocol described by Subbarayan PR and colleagues (doi: 10.21... |
50,040 | Fallopian Tube Epithelial Cell Culture | 4 | dx.doi.org/10.17504/protocols.io.bu4ynyxw | https://www.protocols.io/view/fallopian-tube-epithelial-cell-culture-bu4ynyxw | Ramlogan Sowamber, Melissa Nicole Castillo, Iru Paudel, Sophia HL HL George | TITLE: Fallopian Tube Epithelial Cell Culture
AUTHORS: Ramlogan Sowamber, Melissa Nicole Castillo, Iru Paudel, Sophia HL HL George
[DESCRIPTION]
The purpose of this protocol is to grow primary fallopian tube epithelial cells as 2D culture.
This protocol explains the method of culturing and maintaining fallopian tub... | ["[Dissociating cells from cell culture plate] Dissociate FTE cells from tissue culture plates", "[Dissociating cells from cell culture plate] Wash cells with wash solution (PBS +1% P/S)", "[Dissociating cells from cell culture plate] Aspirate wash solution with an autoclaved borosilicate glass pipette", "[Dissociating... |
null | null | null | dx.doi.org/10.17504/protocols.io.qeydtfw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Non-enzymatic, high-gain signal amplification methods with single-cell, single-molecule resolution are in great need. We present click-amplifying FISH (clampFISH) for the fluorescent detection of RNA that combines the specificity of oligonucleotides with bioorthogonal click c... | [] |
83,090 | Glia-Free Cortical Neuron Culture | 4 | dx.doi.org/10.17504/protocols.io.36wgq3r35lk5/v1 | https://www.protocols.click/view/glia-free-cortical-neuron-culture-cvdsw26e | Justin T Savage, Juan Ramirez, Dolores Irala, Cagla Eroglu | TITLE: Glia-Free Cortical Neuron Culture
AUTHORS: Justin T Savage, Juan Ramirez, Dolores Irala, Cagla Eroglu
[DESCRIPTION]
Protocol for feeding neuronal cultures with astrocyte-conditioned media and staining them for synapses.
[STEPS]
SECTION: Preparation of Coverslips (day before prep)
5. Flame sterilize the forceps... | ["[Preparation of Coverslips (day before prep)] Flame sterilize the forceps after spraying with ethanol.", "[Preparation of Coverslips (day before prep)] Wash coverslips with ddH2O in a large petri dish (150 x 15 mm).", "[Preparation of Coverslips (day before prep)] Set coverslips in a large petri dish (150 x 15 mm). C... |
89,713 | Ten(10)X-compatible Combinatorial Indexing ATAC sequencing (txci-ATAC-seq) | 1 | dx.doi.org/10.17504/protocols.io.dm6gp3o68vzp/v1 | https://www.protocols.io/view/ten-10-x-compatible-combinatorial-indexing-atac-se-c3urynv6 | Hao Zhang, Ryan Mulqueen, Andrew Adey, Darren Cusanovich | TITLE: Ten(10)X-compatible Combinatorial Indexing ATAC sequencing (txci-ATAC-seq)
AUTHORS: Hao Zhang, Ryan Mulqueen, Andrew Adey, Darren Cusanovich
[DESCRIPTION]
The txci-ATAC-seq method is a large-scale single-cell ATAC-seq technique that combines the Tn5-based pre-indexing with the 10X Chromium-based microfluidic ba... | ["[txci-ATAC-seq: Preparing nuclei] Add 3 ml RSB washing buffer to an empty 15 ml tube for each sample.", "[txci-ATAC-seq: Preparing nuclei] Transfer 1 ml nuclei stored in the freezing buffer to the 15 ml tube containing 3 ml RSB washing buffer.", "[txci-ATAC-seq: Preparing nuclei] Pellet the nuclei at 500 RCF for 10 m... |
62,388 | Workflow for human placental ECM proteomics | 3 | dx.doi.org/10.17504/protocols.io.5qpvob7k7l4o/v1 | https://www.protocols.io/view/workflow-for-human-placental-ecm-proteomics-b86urzew | Anthony Saviola, Kirk C Hansen | TITLE: Workflow for human placental ECM proteomics
AUTHORS: Anthony Saviola, Kirk C Hansen
[DESCRIPTION]
Described here is the workflow used by the Female Reproductive Tissue Mapping Center at UCSD to generate extracellular matrix proteomics (ECM) data from human placenta.
[STEPS] | [] |
28,039 | FLUORESCENCE LOSS ASSAY | null | dx.doi.org/10.17504/protocols.io.7mfhk3n | null | Alexander Niederau, Despoina Trasanidou | TITLE: FLUORESCENCE LOSS ASSAY
AUTHORS: Alexander Niederau, Despoina Trasanidou
[STEPS]
?. [Day 1 (=Transformation -> ONC in 96-well plate)]
50ul of chemically competent E. coli DH10B_gfp cells were transformed (heat-shock: 42°C, 30sec) with 3ng plasmid (Cplasmid*2ul=3ng/ul*x -> x=...ul=2ul undiluted plasmid + rest ul... | ["[Day 1 (=Transformation -> ONC in 96-well plate)]\n50ul of chemically competent E. coli DH10B_gfp cells were transformed (heat-shock: 42°C, 30sec) with 3ng plasmid (Cplasmid*2ul=3ng/ul*x -> x=...ul=2ul undiluted plasmid + rest ul MQ) and recovered in 450 ul LB for 1h at 37°C. (PC = E. coli DH10B_gfp + pACYC184) (NC =... |
31,742 | Wuhan coronavirus (2019-nCoV) real-time RT-PCR N gene 2020 (Wuhan-N) | null | dx.doi.org/10.17504/protocols.io.ba86ihze | null | Judy A. Northill, Ian Mackay | TITLE: Wuhan coronavirus (2019-nCoV) real-time RT-PCR N gene 2020 (Wuhan-N)
AUTHORS: Judy A. Northill, Ian Mackay
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><ul style = "list-style-type:disc;"><li style = "counter-reset:ol0;list-style-type:disc;">A real-time RT-PCR to detect the "novel Wuhan" b... | ["[Mix]\nOligonucleotides ABC1Oligo NameSequence 5'-3'Location based on NC_045512*2Wuhan-TM2020ForTCGTGCTACAACTTCCTCAAG28648-286683Wuhan-TM2020Probe6FAM-CCGCCTCTGCTCCCTTCTGC-BHQ128714-286954Wuhan-TM2020RevCTGCCWGGAGTTGAATTTCTTG28780-28759\nABC1Oligo NameSequence 5'-3'Location based on NC_045512*2Wuhan-TM2020ForTCGTGCT... |
null | null | null | dx.doi.org/10.17504/protocols.io.q27dyhn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>PROSPERO protocol</p>
<p>Link: http://www.crd.york.ac.uk/PROSPERO/display_record.php?ID=CRD42017078712</p>
<p> </p>
[GUIDELINES]
<p>Citation<br />Turki Albatti, Saleh Al Salehi, Fahad Bashiri, Muddathir Hamad, Haya Al-Joudi, Hadeel Daghash,<br />Jeremy Varnham, Yasser Amer. ... | [] |
107,087 | Formation of ventral midbrain Assembloid/Organoids | 0 | dx.doi.org/10.17504/protocols.io.n2bvjn175gk5/v1 | https://www.protocols.io/view/formation-of-ventral-midbrain-assembloid-organoids-dktp4wmn | Regine Tipon, Gist Croft | TITLE: Formation of ventral midbrain Assembloid/Organoids
AUTHORS: Regine Tipon, Gist Croft
[DESCRIPTION]
Brain organoids are three-dimensional (3D) structures derived from human pluripotent stem cells (hPSCs) that reflect early brain organization. Compared with traditional cell cultures, brain organoids offer a more ... | ["[Formation of ventral midbrain Assembloid/Organoids] Following Croft Lab edited vmDA protocol (dx.doi.org/10.17504/protocols.io.yxmvmebdog3p/v1, ventral midbrain organoids are dissociated at day 33 using the Worthington Kit protocol (dx.doi.org/10.17504/protocols.io.j8nlk8dbxl5r/v1) into single cell suspension", "[Fo... |
37,850 | DNA Extraction (solid tissues) | 4 | dx.doi.org/10.17504/protocols.io.rm7vz8ee8vx1/v1 | https://www.protocols.io/view/dna-extraction-solid-tissues-bg72jzqe | Dakota Betz | TITLE: DNA Extraction (solid tissues)
AUTHORS: Dakota Betz
[DESCRIPTION]
How to complete DNA extraction from solid tissues (fresh, stored in ethanol, or frozen).
[BEFORE_START]
Use 75% ethanol and 10% bleach to clean the lab bench, tube racks, pipettes, centrifuges (mini and large), and vortex before taking out any r... | ["[Scale Protocol] Optionally, follow along with this supplementary tutorial video as you perform the protocol:\n \nDouble check that you have appropriately scaled this protocol for the number of samples you need to prep (use scale option after clicking \"run\").", "[Digestion] Create a master-mix for this step if you'... |
63,759 | Mitochondrial ROS Determination | 4 | dx.doi.org/10.17504/protocols.io.n92ldzj6nv5b/v1 | https://www.protocols.io/view/mitochondrial-ros-determination-cahpsb5n | mitsjoecohen | TITLE: Mitochondrial ROS Determination
AUTHORS: mitsjoecohen
[DESCRIPTION]
Reactive oxygen species (ROS) is a by-product of biological aerobic metabolism, including oxygen ions, peroxides, and oxygen-containing free radicals. More and more studies have proved that ROS is a messenger molecule of multiple signal pathw... | [] |
32,868 | Love Data Week 2020 at CMU Libraries - Valentine's Day Dessert Recipes | null | dx.doi.org/10.17504/protocols.io.bcccissw | null | Hannah Gunderman, Angelina Spotts, Emma Slayton | TITLE: Love Data Week 2020 at CMU Libraries - Valentine's Day Dessert Recipes
AUTHORS: Hannah Gunderman, Angelina Spotts, Emma Slayton
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">At CMU Libraries, each year we celebrate Love Data Week (LDW) with events, workshops, speakers, and activities to... | [] |
63,065 | ERGA_AssemblyProtocol_Template | 5 | null | https://www.protocols.io/view/erga-assemblyprotocol-template-b9tzr6p6 | ann.mccartney | TITLE: ERGA_AssemblyProtocol_Template
AUTHORS: ann.mccartney
[DESCRIPTION]
ERGA_Assembly_Strategy
Abstract written by SAC Committee.
[GUIDELINES]
Any Guidelines Recommended by SAC
[STEPS]
SECTION: Computing Environment Used
1.
Please enter all details of the compute system your analyses was carried out on
SE... | ["[Computing Environment Used] Please enter all details of the compute system your analyses was carried out on", "[Data Cleaning] Please enter instructions on how your cleaned your data\nSoftware\nSummary of approach\nVersion\nCode\nSystem Requirements\nAdditional Tips for users", "[Assembly Polishing] Please enter ins... |
68,881 | In vitro LRRK2 autophosphorylation | 1 | dx.doi.org/10.17504/protocols.io.81wgb6m91lpk/v1 | https://www.protocols.io/view/in-vitro-lrrk2-autophosphorylation-cfhrtj56 | Xinbo Wang, Pietro De Camilli | TITLE: In vitro LRRK2 autophosphorylation
AUTHORS: Xinbo Wang, Pietro De Camilli
[DESCRIPTION]
This protocol details methods for the in vitro LRRK2 autophosphorylation assay.
[STEPS]
SECTION: In vitro LRRK2 autophosphorylation
1. Set up the reaction mixture in a 1.7 mL Eppendorf tube with 1.4 mL purified LRRK2 protei... | ["[In vitro LRRK2 autophosphorylation] Set up the reaction mixture in a 1.7 mL Eppendorf tube with 1.4 mL purified LRRK2 protein, 1x kinase buffer with 1 millimolar (mM) ATP and 0.01 U/µL GST-Prescission Protease (to remove the Flag tag).", "[In vitro LRRK2 autophosphorylation] Incubate samples at 4 °C.", "[In vitro ... |
53,307 | Recombinant protein expression and purification of Taq DNA polymerase | 4 | dx.doi.org/10.17504/protocols.io.bya3psgn | https://www.protocols.io/view/recombinant-protein-expression-and-purification-of-bya3psgn | Maira Rivera, Javiera Reyes , Javiera A Avilés , Amparo Núñez, Fernan Federici, Cesar A Ramirez-Sarmiento | TITLE: Recombinant protein expression and purification of Taq DNA polymerase
AUTHORS: Maira Rivera, Javiera Reyes , Javiera A Avilés , Amparo Núñez, Fernan Federici, Cesar A Ramirez-Sarmiento
[DESCRIPTION]
This is a slightly modified and simplified version of a protocol by Thomas G.W. Graham et al, which is ava... | ["[DAY 1 – Plasmid transformation] Transform 100 ngof plasmid containing Taq DNA polymerase into E. coli C41 competent cells using either heat shock or electroporation.", "[DAY 1 – Plasmid transformation] Spread transformed cells in LB Agar plates supplemented with 0.05 mg/mLKan. Grow plate overnight at 37 °C.", "[DAY ... |
58,403 | Taxon group: Terrestrial Arthropods smaller than 5mm (TSS3) | 1 | dx.doi.org/10.17504/protocols.io.14egn724mv5d/v1 | https://www.protocols.io/view/taxon-group-terrestrial-arthropods-smaller-than-5m-b5abq2an | Lyndall Pereira da Conceicoa, Olga Sivell, Laura Sivess, Chris Fletcher, Gavin R. Broad, Liam Crowley, Inez Januszczak | TITLE: Taxon group: Terrestrial Arthropods smaller than 5mm (TSS3)
AUTHORS: Lyndall Pereira da Conceicoa, Olga Sivell, Laura Sivess, Chris Fletcher, Gavin R. Broad, Liam Crowley, Inez Januszczak
[DESCRIPTION]
This is part of the collection "DToL Taxon-specific Standard Operating Procedure (SOP) for the Terrestrial and... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.nvzde76 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Purpose of this protocol is to assess the enzymatic activity of glycosidases using fluorophores conjugated to substrates of interest (such as cellobiose or xylobiose). Once the enzyme of interest cleaves substrate, the fluorophore is released enabling quantification of enzyma... | [] |
106,574 | Immunohistochemistry | 0 | dx.doi.org/10.17504/protocols.io.rm7vzjem2lx1/v1 | https://www.protocols.io/view/immunohistochemistry-dkbn4sme | Tiziano Balzano, Javier Blesa, Jose Obeso | TITLE: Immunohistochemistry
AUTHORS: Tiziano Balzano, Javier Blesa, Jose Obeso
[DESCRIPTION]
Immunohistochemistry protocol
[STEPS]
1. Wash sections 3 x 5 min with Tris buffered solution (TB).
2. Antigen retrieval: incubate secions 30 min in citrate buffer at 37°C.
3. Wash sections 3 x 5 min with TB.
4. Wash sections ... | ["Wash sections 3 x 5 min with Tris buffered solution (TB).", "Antigen retrieval: incubate secions 30 min in citrate buffer at 37°C.", "Wash sections 3 x 5 min with TB.", "Wash sections 10 min with Tris buffered-saline solution (TBS).", "Endogenous peroxidase blocking: incubate sections in a solution consisting of 3% H... |
null | null | null | dx.doi.org/10.17504/protocols.io.c4hyt5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
As used in Rich, Konstantinidis, and DeLong. 2008. <br /><br />Rich VI., Konstantinidis K., DeLong EF. Design and testing of 'genome-proxy' microarrays to profile marine microbial communities. <a href="http://www.ncbi.nlm.nih.gov/pubmed/18028413" target="_blank">http:/... | [] |
33,758 | RNA Extraction with Trizol | 1 | dx.doi.org/10.17504/protocols.io.6qpvrop22vmk/v1 | https://www.protocols.io/view/rna-extraction-with-trizol-bc76izre | Dakota Betz | TITLE: RNA Extraction with Trizol
AUTHORS: Dakota Betz
[DESCRIPTION]
This is a protocol for RNA extractions (using Trizol). A maximum of 3 samples can be extracted at once using this protocol. The entire protocol should be run in the fumehood. This protocol is time- and temperature-sensitive, so read all instructions ... | ["[Homogenize Tissues] Add 770 uL of Trizol to bead bashing tube (1 per sample).", "[Homogenize Tissues] Pour tissue into a clean Petri dish, keep on cooling block (flat ice pack).", "[Homogenize Tissues] Transfer pieces of tissue to bead bashing tube, blot RNAlater with a kim tissue. \nMay be a very small amount of ti... |
63,393 | Live Well CBD Gummies *Effective* Curing All Your Health Issues In Very Little Time | 3 | dx.doi.org/10.17504/protocols.io.ewov1nxy2gr2/v1 | https://www.protocols.io/view/live-well-cbd-gummies-effective-curing-all-your-he-b959r896 | jerritdsuza | TITLE: Live Well CBD Gummies *Effective* Curing All Your Health Issues In Very Little Time
AUTHORS: jerritdsuza
[DESCRIPTION]
Live Well CBD Gummies are a tasty, squishy candy-like CBD fundamental mix that provides the body with great nutrients derived from organic hemp extracted from 100% pure CBD oil!... | [] |
55,628 | Hematoxylin & Eosin Protocol For Leica ST5020 Automated Stainer | 1 | dx.doi.org/10.17504/protocols.io.x54v9mozqg3e/v2 | https://www.protocols.io/view/hematoxylin-amp-eosin-protocol-for-leica-st5020-au-b2jkqckw | Angela Denn | TITLE: Hematoxylin & Eosin Protocol For Leica ST5020 Automated Stainer
AUTHORS: Angela Denn
[DESCRIPTION]
This Hematoxylin and Eosin protocol is for the Leica ST5020 Automated multistainer. You can use it as a guide to developing your own protocol, catered to the needs of your researchers. This template can be mod... | ["[H&E Stain] Reagent layout for multi stainer use.", "[H&E Stain] Program for H&E protocol."] |
null | null | null | dx.doi.org/10.17504/protocols.io.hgwb3xe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes the generation of mFwe Knockout n2a cells. It is from 'Flower Ca<sup>2+</sup> channel in CME and ADBE' of Yao CK et al.</p>
<div>
<div>
<p> </p>
<p>Please see the manuscript for the full method details.</p>
</div>
</div>
[STEPS]
?.
?.
?.
?.
?.
?.... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.nyhdft6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The use of genetically encoded ‘self-labeling tags’ with chemical fluorophore ligands enables rapid labeling of specific cells in neural tissue. To improve the chemical tagging of neurons, we synthesized and evaluated new fluorophore ligands based on Cy, Janelia Fluor, Alexa ... | [] |
16,788 | Air and floral sampling method and results including thunderstorm | 1 | dx.doi.org/10.17504/protocols.io.umueu6w | https://www.protocols.io/view/air-and-floral-sampling-method-and-results-includi-umueu6w | Jane E.M. Gibbs, Jane E.M. Gibbs | TITLE: Air and floral sampling method and results including thunderstorm
AUTHORS: Jane E.M. Gibbs, Jane E.M. Gibbs
[DESCRIPTION]
Air and floral sampling method and results including thunderstorm sampling
[STEPS] | [] |
42,653 | lysis buffer裂解基因组 | 1 | null | https://www.protocols.io/view/lysis-buffer-bmv5k686 | 张 雪 | TITLE: lysis buffer裂解基因组
AUTHORS: 张 雪
[STEPS]
?. 〔0.5µl Proteinase K＋20µl lysis buffer，1:40混合〕/embryo，55°C，5h
55 °C
?. 95°C，15min，此为stock
95 °C
?. 吸取3µl stock+47µl ddH2O，此为work | ["〔0.5µl Proteinase K＋20µl lysis buffer，1:40混合〕/embryo，55°C，5h\n55 °C", "95°C，15min，此为stock\n95 °C", "吸取3µl stock+47µl ddH2O，此为work"] |
37,582 | Ambient sample storage system of field-collected insect samples for genomics | null | dx.doi.org/10.17504/protocols.io.bgxnjxme | https://www.protocols.io/view/ambient-sample-storage-system-of-field-collected-i-bgxnjxme | Roland Wouters, Sam Mugford, Saskia Hogenhout | TITLE: Ambient sample storage system of field-collected insect samples for genomics
AUTHORS: Roland Wouters, Sam Mugford, Saskia Hogenhout
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Population genomics studies require the purification of high-quality DNA from field collected samples for subsequ... | ["Measure the pipette tip against the Eppendorf tube, and cut off the tip of the pipette tip. The remaining length of the pipette tip should fit inside the Eppendorf tube, with the wide end of the tube fitting tightly against the inside of the tube.", "With the tip removed from the tube, add approximately 100ul of sili... |
null | null | null | dx.doi.org/10.17504/protocols.io.ki6cuhe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div title="Page 53">
<div>
<div>
<p>Standard hematological analyses</p>
<p>EDTA-anticoagulated blood was used for cytometric analysis using a whole blood counter Sysmex XE 2100® (Sysmex,Kobe, Japan) to obtain a whole blood count. Fibrinogen levels were determined with an ACL-90... | [] |
80,843 | Using Amira to manually segment organelles in vEM for machine learning | 1 | dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v2 | https://www.protocols.io/view/using-amira-to-manually-segment-organelles-in-vem-cs7jwhkn | Grace Park, Nora Forknall, Larissa Heinrich, Henrique Ludwig, Ruchi Parekh, Alyson Petruncio, Jacquelyn Price, Diana Ramirez, rymert, Stephan Saalfeld, Alia Suleiman, Rebecca Vorimo, Aubrey Weigel | TITLE: Using Amira to manually segment organelles in vEM for machine learning
AUTHORS: Grace Park, Nora Forknall, Larissa Heinrich, Henrique Ludwig, Ruchi Parekh, Alyson Petruncio, Jacquelyn Price, Diana Ramirez, rymert, Stephan Saalfeld, Alia Suleiman, Rebecca Vorimo, Aubrey Weigel
[DESCRIPTION]
In this protocol we d... | ["[Protocol Introduction] The purpose of this protocol is to document the unique annotation method and style used by CellMap Project Team to annotate organelles using Amira-Avizo (Thermo Fisher Scientific). We defined 37 organelle subclasses to annotate within cell and tissue data and classified them. The definitions u... |
37,126 | Quantification de la callose dans les filaments de P. patens par microscopie confocale | null | dx.doi.org/10.17504/protocols.io.bghejt3e | https://www.protocols.io/view/quantification-de-la-callose-dans-les-filaments-de-bghejt3e | Yoan Coudert, Arthur Muller | TITLE: Quantification de la callose dans les filaments de P. patens par microscopie confocale
AUTHORS: Yoan Coudert, Arthur Muller
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Culture]
Faire une culture de colonie sur milieu BCD (AT) pendant 15 jours en boîte carrée (10 x 10 cm)
?. [Aniline blue stain... | ["[Culture]\nFaire une culture de colonie sur milieu BCD (AT) pendant 15 jours en boîte carrée (10 x 10 cm)", "[Aniline blue staining]\nPréparer la solution de travail en diluant la solution stock d’aniline bleu 1:3 (v :v) dans du tampon phosphate pH 8,5", "[Aniline blue staining]\nRemplir les puits d’une plaque 48 pui... |
59,801 | FLASH-seq UMI protocol | 4 | dx.doi.org/10.17504/protocols.io.bp2l619rdvqe/v3 | https://www.protocols.io/view/flash-seq-umi-protocol-b6mzrc76 | Simone Picelli, Vincent Hahaut | TITLE: FLASH-seq UMI protocol
AUTHORS: Simone Picelli, Vincent Hahaut
[DESCRIPTION]
The single-cell RNA-sequencing (scRNA-seq) field has evolved tremendously since the first paper was published back in 2009. While the first methods analysed just a handful of cells, the throughput and performance rapidly increased o... | ["[Prepare lysis mix] Prepare the following lysis mix:\n ReagentReaction concentrationVolume (µl)384-well plateTriton-X100 (10% v/v)0.2%0.0208.448dNTP mix (25 mM each)6 mM0.240101.376STRT-P1-T31 oligo (100 µM)1.8 mM0.0187.603RNAse inhibitor (40 U/µl)1.2 U/µl0.03012.672DTT (100 mM)1.2 mM0.0125.069dCTP (100 µM)9 mM0.0... |
97,424 | RNA Slide Preparation Protocol (FFPE) for nanostring DSP - GeoMx - Human Ovary samples | 4 | dx.doi.org/10.17504/protocols.io.bp2l624bdgqe/v1 | https://www.protocols.io/view/rna-slide-preparation-protocol-ffpe-for-nanostring-dbdq2i5w | Nicolas Martin | TITLE: RNA Slide Preparation Protocol (FFPE) for nanostring DSP - GeoMx - Human Ovary samples
AUTHORS: Nicolas Martin
[DESCRIPTION]
This protocol is designed for RNA slide preparation for formalin-fixed tissue.
[GUIDELINES]
This is the default protocol for slide preparation by Nanostring.
IMPORTANT:
Take care to ... | ["Prepare reagents\n\nPrepare the reagents using the dilution instructions (see Table 1).\nUse DEPC- treated water for all dilutions. The actual volume of\nreagents used in the protocol will vary – the volumes to prepare in Table 1 are suggestions.\n\nTable 1: Reagent prep for RNA slide preparation\n\n Reagent ... |
85,816 | Sampling leaf tissue for analysis of NPQ Relaxation using Technologica Chlorophyll Fluorescence Imager Data. | 4 | null | https://www.protocols.io/view/sampling-leaf-tissue-for-analysis-of-npq-relaxatio-cx2yxqfw | Lynn Doran | TITLE: Sampling leaf tissue for analysis of NPQ Relaxation using Technologica Chlorophyll Fluorescence Imager Data.
AUTHORS: Lynn Doran
[DESCRIPTION]
Sampling leaf tissue for analysis of NPQ Relaxation using Technologica Chlorophyll Fluorescence Imager Data.
[STEPS]
SECTION: Leaf Tissue Sampling
1. Cut #1 Whatman f... | ["[Leaf Tissue Sampling] Cut #1 Whatman filter paper into small squares that are just bigger than the well on a 24-well culture plate.", "[Leaf Tissue Sampling] Using a #2 Humboldt cork borer, take leaf tissue samples from each plot for each technical replicate. Hold the leaf flat against the rubber stopper, press the... |
83,845 | Working in AnVIL: A Clinical Sequencing Evidence-Generating Research (CSER) consortium perspective. | 5 | dx.doi.org/10.17504/protocols.io.q26g7ye68gwz/v2 | https://www.protocols.click/view/working-in-anvil-a-clinical-sequencing-evidence-ge-cv5dw826 | Richard Green, Kathleen Ferar, Jeffrey Ou, Michael Schatz, Stephen Mosher, David R Crosslin, Gail P Jarvik | TITLE: Working in AnVIL: A Clinical Sequencing Evidence-Generating Research (CSER) consortium perspective.
AUTHORS: Richard Green, Kathleen Ferar, Jeffrey Ou, Michael Schatz, Stephen Mosher, David R Crosslin, Gail P Jarvik
[DESCRIPTION]
Analysis, Visualization, and Informatics Lab-space (AnVIL) is a powerful new Genom... | ["[Introduction] AnVIL is a powerful data-sharing genomics platform that allows for data processing and analysis to be shared in the cloud. The goal of this protocol is to get new users that are relatively new to AnVIL up and running. The AnVIL is a cloud-centric platform that provides tools to interface with local har... |
92,872 | Analogizing the Nexus of Nutritional Status and Oral Health in Children of Pre-School age in Ranchi City of East India: A Protocol | 4 | dx.doi.org/10.17504/protocols.io.bp2l6xe9zlqe/v1 | https://www.protocols.io/view/analogizing-the-nexus-of-nutritional-status-and-or-c6xgzfjw | Arunima, dr annapurna ahuja, drvipinahuja, nilima dr nilima thosar | TITLE: Analogizing the Nexus of Nutritional Status and Oral Health in Children of Pre-School age in Ranchi City of East India: A Protocol
AUTHORS: Arunima, dr annapurna ahuja, drvipinahuja, nilima dr nilima thosar
[DESCRIPTION]
This contemporary research purposes to analogize the nexus between the Body mass index (BMI... | ["[Introduction] Anthropometric measurements are the human body\nmeasurements which quantify us with vital indicators of nutritional status in\nchildren and adults. These include overall health, nutritive adequacy, growth\nand development measurements over time in growing children and adults. Body\nmass index (BMI) mea... |
null | null | null | dx.doi.org/10.17504/protocols.io.jvgcn3w | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?. | [] |
24,104 | Biochemical Measures of Neuropathy - Lowry Protein Assay | null | dx.doi.org/10.17504/protocols.io.3sggnbw | null | Eva Feldman | TITLE: Biochemical Measures of Neuropathy - Lowry Protein Assay
AUTHORS: Eva Feldman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">Oxidative stress is highly correlated with the metabolic changes caused by hyperglycem... | ["[Performing the Assay:]\n1. Thaw samples on ice. 2. If samples contain detergent: add 20ul of reagent S to each ml for reagent A 3. Prepare standard as follows: 4. Pipet 5 µl of standards and samples into plate. 5. Add 25 µl of reagent A to each well. 6. Add 200 µl reagent B to each well. 7. Place plate in reader an... |
20,633 | Adult mouse skin dissociation protocol (on ice) | null | dx.doi.org/10.17504/protocols.io.ydzfs76 | null | Andrew Potter | TITLE: Adult mouse skin dissociation protocol (on ice)
AUTHORS: Andrew Potter
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol was developed to dissociate adult (8-10 wk) mouse skin "on ice". It utilizes two layers of digestion with a </span><span style = "font-style:italic;">Baci... | ["[Isolating tissue]\nAfter euthanizing mouse, remove hair using Nair: dab with Nair, wait 30 secs, wipe with wet paper towel.", "[Isolating tissue]\nIsolate tissue and place in ice-cold hypothermosol.", "[Isolating tissue]\nScrape off underlying layer of fatty / connective tissue using scalpel before proceeding.", "[I... |
14,737 | Murine CD8 T cell transduction | 1 | dx.doi.org/10.17504/protocols.io.smrec56 | https://www.protocols.io/view/murine-cd8-t-cell-transduction-smrec56 | Kristin Anderson | TITLE: Murine CD8 T cell transduction
AUTHORS: Kristin Anderson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">CD8 T cells can be transduced to express genes transferred by retroviral transduction. This protocol outlines the steps for generating retrovirus from PLAT-E packaging cells to transduce p... | ["[Day 0: Prepare PLAT-E cells for transfection]\n1. Gently remove PLAT-E media and rinse PLAT-E cells with 1x DPBS.2. Gently remove PBS and add 0.05% Trypsin. Trypsinize at 37C for 1-2 minutes or until cells being to lift off the plate with a gentle tap.3. Dilute and inactivate trypsin with 10ml PLAT-E media.Transfer ... |
16,843 | Protein preparation for LC-MS/MS analysis | null | dx.doi.org/10.17504/protocols.io.upjevkn | null | Lihui Li | TITLE: Protein preparation for LC-MS/MS analysis
AUTHORS: Lihui Li
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is with regard to quantitative proteomics analysis to identify biomarkers of chronic myofascial pain and therapeutic targets of dry needling in a rat model of myofascial t... | ["The SDT lysis buffer was added to the sample and transferred to 2ml tubes with quartz sand consisting of 1/4-inch ceramic beads (MP 6540-424 for tissue samples).", "The lysate was homogenized twice for 60 s using an MP homogenizer (24×2, 6.0M/S).", "The homogenate was sonicated and then boiled for 15min.", "After cen... |
53,317 | iBlot2--CHEM 584 | 1 | dx.doi.org/10.17504/protocols.io.bybdpsi6 | https://www.protocols.io/view/iblot2-chem-584-bybdpsi6 | Ken Christensen | TITLE: iBlot2--CHEM 584
AUTHORS: Ken Christensen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Transferring your proteins from your SDS-PAGE gel to a nitrocellulose membrane for western blot is quick and straightforward.</div></div>
[STEPS]
?. [iBlot2 Transfer]
Watch the video about setting up an... | ["[iBlot2 Transfer]\nWatch the video about setting up and running your transfer to nitrocellulose at the following link: https://videos.thermofisher.com/detail/video/6059971760001/how-to-perform-a-western-blot-dry-transfer-using-the-invitrogen-iblot-2-dry-blotting-system"] |
98,411 | Enterovirus D68 3C protease large scale purification protocol | 1 | dx.doi.org/10.17504/protocols.io.n92ld8yd7v5b/v1 | https://www.protocols.io/view/enterovirus-d68-3c-protease-large-scale-purificati-dccj2sun | Korvus Wang, michael fairhead, Eleanor Williams | TITLE: Enterovirus D68 3C protease large scale purification protocol
AUTHORS: Korvus Wang, michael fairhead, Eleanor Williams
[DESCRIPTION]
This protocol details the expression and purification of enterovirus D68 3C protease construct bearing a C-terminal His-tag at large scale (>6L)
[GUIDELINES]
Construct / plasmid... | ["[Plasmid Transformation] Transform the D68EV3C construct (Addgene plasmid #204817) into BL21(DE3) and store a glycerol stock of this at -80 °C", "[Protein Purifcation] Perform IMAC to extract target protein from the lysed cell mixture", "[Protein Purifcation] Wash the column with 10 CV of wash buffer 1, then 10 CV w... |
21,676 | SYSB 3036 W07: Pan-genomics | null | dx.doi.org/10.17504/protocols.io.zekf3cw | null | Frank Aylward | TITLE: SYSB 3036 W07: Pan-genomics
AUTHORS: Frank Aylward
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Get the data]
First we need to get some data to start with. I have already prepared some starting files and put them on a GitHub repository, so we can download it using the following command:git clone... | ["[Get the data]\nFirst we need to get some data to start with. I have already prepared some starting files and put them on a GitHub repository, so we can download it using the following command:git clone https://github.com/faylward/pangenomics_tutorialAfter this command finishes you should see a new folder called \"pa... |
48,040 | QuPath Digital Quantification of Liver Immune Cells | 5 | dx.doi.org/10.17504/protocols.io.bs6gnhbw | https://www.protocols.io/view/qupath-digital-quantification-of-liver-immune-cell-bs6gnhbw | Xinle Wang, Catia Perciani, Xue-Zhong Ma, Chao Jiang, Justin Manuel, Sai Chung, Cornelia Thoeni, Trevor McKee, Ian McGilvray, Sonya Macparland | TITLE: QuPath Digital Quantification of Liver Immune Cells
AUTHORS: Xinle Wang, Catia Perciani, Xue-Zhong Ma, Chao Jiang, Justin Manuel, Sai Chung, Cornelia Thoeni, Trevor McKee, Ian McGilvray, Sonya Macparland
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Digital image analysis is a widely employ... | ["[Download, Import and Organize Images]\nDownload open-source QuPath software from http://qupath.github.io. To avoid incompatible features in newer versions of the software, refrain from changing software versions during the same analysis.", "[Sample Image Quality Control]\nBefore quantification analysis, it is import... |
101,299 | OSU TriState SenNet Processing and Storing of a Normal Donor Heart | 0 | dx.doi.org/10.17504/protocols.io.14egn66kql5d/v1 | https://www.protocols.io/view/osu-tristate-sennet-processing-and-storing-of-a-no-de6t3hen | Sean D. Stacey, Brenda F. Reader, Lorena Rosas, Victor Peters, Ana L. Mora, Mauricio Rojas | TITLE: OSU TriState SenNet Processing and Storing of a Normal Donor Heart
AUTHORS: Sean D. Stacey, Brenda F. Reader, Lorena Rosas, Victor Peters, Ana L. Mora, Mauricio Rojas
[DESCRIPTION]
This protocol describes the processing and storing of normal donor heart by the Comprehensive Transplant Center (CTC) Human Tissue ... | ["[Objective] To preserve heart tissue for further downstream cellular, protein, RNA, or DNA analyses.", "[Preparation] In the biosafety cabinet (BSC), place three underpads and all needed equipment, including biohazard receptacles, surgical kits, and specimen holders. Before beginning processing samples, check that al... |
23,275 | DABCO Mounting Slide Protocol for Drosophila melanogaster embryos | null | dx.doi.org/10.17504/protocols.io.2yjgfun | null | Ashley Albright | TITLE: DABCO Mounting Slide Protocol for Drosophila melanogaster embryos
AUTHORS: Ashley Albright
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for mounting Drosophila melanogaster embryos stored in PBS or PBT onto slides for conventional fluorescence and/or confocal microscopy. </div><di... | ["[Mount Slides]\nTake off as much liquid as you can, resuspend embryos in an arbitrary amount of DABCO mountant (depends on how dilute you want the embryos to be, but generally a couple hundred ul). Allow the embryos to settle to at or overnight at before mounting. Embryos can be stored for months/years in mic... |
58,765 | Algal Media Recipe from Cáceres Lab | 3 | null | https://www.protocols.io/view/algal-media-recipe-from-c-ceres-lab-b5mmq446 | Carla Cáceres, Isabella Oleksy | TITLE: Algal Media Recipe from Cáceres Lab
AUTHORS: Carla Cáceres, Isabella Oleksy
[DESCRIPTION]
This is a protocol to make media to grow algae in. In the Duffy Lab, this media is used to grow Ankistrodesmus falactus. This recipe comes from the Cáceres Lab.
[STEPS] | [] |
27,564 | Modified DNeasy PowerWater Kit® protocol for DNA extractions from drinking water samples | null | dx.doi.org/10.17504/protocols.io.66khhcw | null | Solize Vosloo, Maria Sevillano, Ameet Pinto | TITLE: Modified DNeasy PowerWater Kit® protocol for DNA extractions from drinking water samples
AUTHORS: Solize Vosloo, Maria Sevillano, Ameet Pinto
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify"><span>DNA-extractions from drinking water samples a... | ["[PROCESSING OF THE STERIVEX-GP PRESSURE FILTER UNIT]\nOn the surface of a sterile petri dish (Fisher Scientific, Cat. No: FB0875712), cut the PES filter membrane contained in the Sterivex-GP Pressure Filter Unit (EMD Millipore, Cat. No: SVGP01050) into smaller pieces using a sterile scalpel (Fisher Scientific, Cat. N... |
77,177 | Fluorescence_activity_assay_Interlab_Study_PCC_6803 | 4 | dx.doi.org/10.17504/protocols.io.8epv5jdw5l1b/v1 | https://www.protocols.io/view/fluorescence-activity-assay-interlab-study-pcc-680-cpkzvkx6 | maurice.mager1808 | TITLE: Fluorescence_activity_assay_Interlab_Study_PCC_6803
AUTHORS: maurice.mager1808
[DESCRIPTION]
Fluorescence activity assay for Synechococcus PCC 6803 strains during the interlaboratory study published by Mager et al. 2023.
[STEPS]
SECTION: Preculture conditions of the fluorescence activity assay
1. Precultures w... | ["[Preculture conditions of the fluorescence activity assay] Precultures were started from cultures derived from cryoconserved cells after 48h of growth in copper free BG11-PC medium (hereafter referred to as BG11 medium).\n\n \n\n4 Strains were used for the fluorescence activity assay in the Interlab study. All strain... |
76,105 | Set Up Biodata Resource Inventory in Google Colab | 5 | dx.doi.org/10.17504/protocols.io.5jyl89o36v2w/v2 | https://www.protocols.io/view/set-up-biodata-resource-inventory-in-google-colab-cnjhvcj6 | Kenneth Schackart | TITLE: Set Up Biodata Resource Inventory in Google Colab
AUTHORS: Kenneth Schackart
[DESCRIPTION]
This protocol will guide you on how to get everything in place to update the Biodata Resource Inventory.
This protocol describes how to setup Google Colab, connect your Google Drive, and clone the repository.
Some of th... | ["[Prepare Google Drive] In your Google Drive home directory, create a new folder called GitHub.\n\nInside the GitHub folder, create another folder called biodata_resource_inventory.", "[Connect Colab to Drive] Go to Google Colab.\n\nIf you need to change the account you are using, close the pop up by clicking Cancel a... |
61,896 | Guardian Botanicals Blood Balance Australia 2022: Does It Work? My Latest Report | 3 | dx.doi.org/10.17504/protocols.io.bp2l6133kvqe/v1 | https://www.protocols.io/view/guardian-botanicals-blood-balance-australia-2022-d-b8pgrvjw | health | TITLE: Guardian Botanicals Blood Balance Australia 2022: Does It Work? My Latest Report
AUTHORS: health
[DESCRIPTION]
Guardian Botanicals Blood Balance Australia, as I might want to think, is a marvelous thing! This pill will assist your body with fixing itself. Here, you trust in your judgment to successfully pick.... | [] |
41,788 | Dawatek COVID protocol | 4 | dx.doi.org/10.17504/protocols.io.bk24kygw | https://www.protocols.io/view/dawatek-covid-protocol-bk24kygw | Leela Raavi, Davina Moossazadeh, Isaac Chadri | TITLE: Dawatek COVID protocol
AUTHORS: Leela Raavi, Davina Moossazadeh, Isaac Chadri
[STEPS]
?. Use oral saliva swab kit to obtain minimum of saliva, maximum
1 mL
2 mL
?. Add of gold nanoparticles and of saliva into 5mL-eppendorf tube. Mix using vortex mixer for .
1 mL
1 mL
?. Place tube into sample holder of... | ["Use oral saliva swab kit to obtain minimum of saliva, maximum\n1 mL\n2 mL", "Add of gold nanoparticles and of saliva into 5mL-eppendorf tube. Mix using vortex mixer for .\n1 mL\n1 mL", "Place tube into sample holder of Raman spectrometer and turn on then press scan.", "Results will display within seconds"] |
44,777 | Automated H&E Staining and Coverslipping (Leica) | 4 | dx.doi.org/10.17504/protocols.io.bpyhmpt6 | https://www.protocols.io/view/automated-h-amp-e-staining-and-coverslipping-leica-bpyhmpt6 | Linda Thomas, Angie Brown, Kerry Wiles | TITLE: Automated H&E Staining and Coverslipping (Leica)
AUTHORS: Linda Thomas, Angie Brown, Kerry Wiles
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This procedure establishes a consistent process for preparing H&E slides from FFPE tissue samples using the automated H&E Leica Stainer and coversli... | ["[Automated Staining and Coverslipping]\nTurn on the Automated Robotic Cover slipper and check levels for mounting media and coverslip. After initializing, retrieve the white brush clip from the Xylene well in the drawer on the front and clip it in place.", "[Automated Staining and Coverslipping]\nTake the needle out ... |
null | null | null | dx.doi.org/10.17504/protocols.io.fuabnse | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A protocol to encapsulate plant protoplasts using a PDMS microfluidic chip. Work was funded by Cambridge Synthetic Biology Strategic Research Initative (SRI) SynBio Fund.</p>
<p>http://www.synbio.cam.ac.uk/synbiofund</p>
[BEFORE_START]
<p>Prepare protoplasts.</p>
[STEPS]
?.... | [] |
70,238 | Protocol collection: Phage DNA isolation and chemical analysis | 2 | dx.doi.org/10.17504/protocols.io.e6nvwj6w2lmk/v1 | https://www.protocols.io/view/protocol-collection-phage-dna-isolation-and-chemic-cgt6twre | Adair Borges | TITLE: Protocol collection: Phage DNA isolation and chemical analysis
AUTHORS: Adair Borges
[DESCRIPTION]
Bacteriophages (phages) are viruses that infect bacteria. Some phages chemically modify their genomes to protect them from degradation by bacterial immune systems. We can detect phage genome modifications with ma... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.m2fc8bn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Background</strong></p>
<p>Atrial fibrillation (AF) is a major risk of ischemic stroke unless treated with anticoagulant. Detection of AF can be difficult because AF is often paroxysmal and asymptomatic. The aim of this study is to develop a screening model for detect... | [] |
32,067 | Modified Andolfatto- reduced rep sequencing | null | dx.doi.org/10.17504/protocols.io.bbjbikin | null | Jenn Coughlan | TITLE: Modified Andolfatto- reduced rep sequencing
AUTHORS: Jenn Coughlan
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Before You Start]
Before you start:·To order enough restriction enzyme for all of your samples. Calculate the total amount needed for all the samples that you plan to do, and order the... | ["[Before You Start]\nBefore you start:·To order enough restriction enzyme for all of your samples. Calculate the total amount needed for all the samples that you plan to do, and order the appropriate amount of restriction enzyme. Ben Blackman did an in silico digest of the Mimulus genome and determined that Csp6I (G^T... |
76,252 | Protocols for the genome assembly and annotation of the Bungarus multicinctus | 2 | dx.doi.org/10.17504/protocols.io.5jyl8j6e9g2w/v1 | https://www.protocols.io/view/protocols-for-the-genome-assembly-and-annotation-o-cnp4vdqw | Boyang Liu, Liangyu Cui, Yue Ma, Diancheng Yang, Yanan Gong, Yanchun Xu, Shuhui Yang, Song Huang | TITLE: Protocols for the genome assembly and annotation of the Bungarus multicinctus
AUTHORS: Boyang Liu, Liangyu Cui, Yue Ma, Diancheng Yang, Yanan Gong, Yanchun Xu, Shuhui Yang, Song Huang
[DESCRIPTION]
Background: Snakes are one of the most important wildlife resources and are widely distributed. Bungarus multicinc... | [] |
81,456 | 10x Protocols: Visium Fresh Frozen Methanol Fixation, H&E Staining & Imaging-- University of Minnesota TMCs (CG000160 Rev C) | 1 | dx.doi.org/10.17504/protocols.io.kxygx96nkg8j/v1 | https://www.protocols.io/view/10x-protocols-visium-fresh-frozen-methanol-fixatio-ctsqwndw | 10x Genomics, Laura J Niedernhofer, David A Bernlohr | TITLE: 10x Protocols: Visium Fresh Frozen Methanol Fixation, H&E Staining & Imaging-- University of Minnesota TMCs (CG000160 Rev C)
AUTHORS: 10x Genomics, Laura J Niedernhofer, David A Bernlohr
[DESCRIPTION]
Protocols from 10x Genomics for Visium Spatial Gene Expression on Fresh Frozen / OCT samples. Completed... | ["10x protocol CG000160, Rev C (Fixation/H&E etc):", "Additional Protocols/Resources\n CG000241, Rev D\n CG000240, Rev D\nhttps://www.10xgenomics.com/support/spatial-gene-expression-fresh-frozen"] |
87,304 | Sanger Tree of Life HMW DNA Extraction: Manual Nucleated Blood Nanobind® | 4 | dx.doi.org/10.17504/protocols.io.5jyl8p2w8g2w/v1 | https://www.protocols.io/view/sanger-tree-of-life-hmw-dna-extraction-manual-nucl-czhgx33w | Pacific Biosciences, Amy Denton, graeme oatley, Caroline Howard | TITLE: Sanger Tree of Life HMW DNA Extraction: Manual Nucleated Blood Nanobind®
AUTHORS: Pacific Biosciences, Amy Denton, graeme oatley, Caroline Howard
[DESCRIPTION]
This protocol describes the manual extraction of HMW DNA from nucleated blood samples intended for long-read sequencing using the Nanobind® tissue kit a... | ["[Laboratory protocol] Add 10–20 μL of nucleated blood to a 1.5 mL Protein LoBind tube.", "[Laboratory protocol] Add 180–190 μL of 1 X PBS for a total volume of 200 μL.", "[Laboratory protocol] Add 20 μL of Proteinase K.", "[Laboratory protocol] Add 20 μL of RNase A.", "[Laboratory protocol] Pulse vortex the blood sam... |
108,085 | The perfect slice - Cutting bread made easy | 0 | dx.doi.org/10.17504/protocols.io.14egn6qyzl5d/v2 | https://www.protocols.io/view/the-perfect-slice-cutting-bread-made-easy-dmsv46e6 | Bread Pitt, Rye-an Reynolds, Crumbelina Jolie, Elon Crust | TITLE: The perfect slice - Cutting bread made easy
AUTHORS: Bread Pitt, Rye-an Reynolds, Crumbelina Jolie, Elon Crust
[DESCRIPTION]
Bread cutting, while seemingly simple, is an art that embodies both precision and mindfulness. "Cutting bread is the simplest form of precision, where a steady hand meets the resistance ... | ["[Prepare to cut] Gather Your Tools: a serrated bread knife (aka \"Loaf Saber\"), a sturdy wooden cutting board, a nice loaf of bread, and a piece of cloth for crum control", "[Prepare to cut] Make sure your bread is at room temperature. Warm bread will squish under pressure, like a marshmallow in a vice. If you’re de... |
69,688 | Hamstring muscle architecture assessed sonographically using wide field of view: a reliability study | 1 | dx.doi.org/10.17504/protocols.io.5qpvorxjdv4o/v1 | https://www.protocols.io/view/hamstring-muscle-architecture-assessed-sonographic-cgaytsfw | Kevin Cronin | TITLE: Hamstring muscle architecture assessed sonographically using wide field of view: a reliability study
AUTHORS: Kevin Cronin
[DESCRIPTION]
Hamstring injuries are very common in field sports. Muscle architecture has been suggested as a risk factor for hamstring strain injury. Various medical imaging techniques (Ma... | [] |
34,395 | Deep learning in rare disease. Detection of tubers in tuberous sclerosis complex | null | dx.doi.org/10.17504/protocols.io.bdt3i6qn | https://www.protocols.io/view/deep-learning-in-rare-disease-detection-of-tubers-bdt3i6qn | Ivan Sanchez Fernandez et al | TITLE: Deep learning in rare disease. Detection of tubers in tuberous sclerosis complex
AUTHORS: Ivan Sanchez Fernandez et al
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Code and results for the article "Deep learning in rare disease. Detection of tubers in tuberous sclerosis complex".</div></di... | [] |
74,561 | MecA detection Protocol | 4 | dx.doi.org/10.17504/protocols.io.dm6gpjdy1gzp/v1 | https://www.protocols.io/view/meca-detection-protocol-ck29uyh6 | Kabir Umar, Idris Abdullahi Nasir, Abdurrahman E Ahmad, Abdullahi Hassan Kawo, Abduqadir Magaji Magashi, Abubakar Umar Anka | TITLE: MecA detection Protocol
AUTHORS: Kabir Umar, Idris Abdullahi Nasir, Abdurrahman E Ahmad, Abdullahi Hassan Kawo, Abduqadir Magaji Magashi, Abubakar Umar Anka
[DESCRIPTION]
Polymerase chain reaction (PCR) was conducted for the detection of MecA gene from the Staphylococcus aureus Isolated from both healthcare wor... | [] |
40,575 | An easy chromatographic method for purification of Immunoglobulin Y (IgY) using HiTrap™ Columns. | 4 | dx.doi.org/10.17504/protocols.io.bju7knzn | https://www.protocols.io/view/an-easy-chromatographic-method-for-purification-of-bju7knzn | Angel Justiz-Vaillant | TITLE: An easy chromatographic method for purification of Immunoglobulin Y (IgY) using HiTrap™ Columns.
AUTHORS: Angel Justiz-Vaillant
[STEPS]
?. Fill the syringe or pump tubing with de-ionized water. Remove the stopper and connect HiTrap™ column to syringe (use the connector supplied).
?. Snap off tab on the column ... | ["Fill the syringe or pump tubing with de-ionized water. Remove the stopper and connect HiTrap™ column to syringe (use the connector supplied).", "Snap off tab on the column outlet.", "Wash out the ethanol with 26 ml of de-ionized water.", "Equilibrate column with 26 ml of binding buffer. The recommended flow rate is 5... |
79,767 | Preparation of Tissue Sections for Proteomic Analysis | 1 | dx.doi.org/10.17504/protocols.io.14egnxjq6l5d/v3 | https://www.protocols.io/view/preparation-of-tissue-sections-for-proteomic-analy-cr5xv87n | Jamie Allen, Angela R.S. Kruse, Audramjudd, Melissa Farrow, Jeff Spraggins | TITLE: Preparation of Tissue Sections for Proteomic Analysis
AUTHORS: Jamie Allen, Angela R.S. Kruse, Audramjudd, Melissa Farrow, Jeff Spraggins
[DESCRIPTION]
Scope:
To describe the procedure for the lysis, reduction/alkylation, trypsin digestion, and clean-up of protein extracts from tissue sections. Lysis will cov... | ["[Tissue Lysis] Place tubes in dry ice for 5 min", "[Tissue Lysis] Defrost tubes on wet ice for5 min and then vortex briefly.", "[Tissue Lysis] Add ice to water in the sonicator to make an icy slurry.", "[Tissue Lysis] Sonicate samples in ice bath for 10 min and vortex.", "[Tissue Lysis] Spin tubes in microcentrifuge ... |
null | null | null | dx.doi.org/10.17504/protocols.io.khpct5n | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.kuqcwvw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.k9dcz26 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes how to set up an embryo collection cage in order to collect fruit fly eggs and how to relabily dispense a consistent number of eggs into food medium for development.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?. | [] |
45,075 | Parsing of NLM metadata in OpenRefine from OJS articles | 5 | dx.doi.org/10.17504/protocols.io.bp9tmr6n | https://www.protocols.io/view/parsing-of-nlm-metadata-in-openrefine-from-ojs-art-bp9tmr6n | Alessandra Moi, carlo.bianchini , Andrea Marchitelli | TITLE: Parsing of NLM metadata in OpenRefine from OJS articles
AUTHORS: Alessandra Moi, carlo.bianchini , Andrea Marchitelli
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocols for parsing metadata of articles harvested from Open Journal Systems (OJS) in order to create entities in WikiData<... | ["[Attività preliminari]\nImport the OAI identifiers and generate the baseurl list:", "[Attività preliminari]\nTest the operation of one of the generated URLs by clicking on the link and verifying that it opens a page with NLM metadata in XML format.Es. https://aibstudi.aib.it/oai?verb=GetRecord&metadataPrefix=nlm&iden... |
38,221 | Isolation of single cells from adherent cell lines using Smart Aliquotor CE | 4 | dx.doi.org/10.17504/protocols.io.bhjmj4k6 | https://www.protocols.io/view/isolation-of-single-cells-from-adherent-cell-lines-bhjmj4k6 | Lucy Kimbley, Rachel Parker, Maaike Sybil Jongen, John Holloway, Emily Swindle, Matthew Rose-Zerilli | TITLE: Isolation of single cells from adherent cell lines using Smart Aliquotor CE
AUTHORS: Lucy Kimbley, Rachel Parker, Maaike Sybil Jongen, John Holloway, Emily Swindle, Matthew Rose-Zerilli
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">We present a method for the isolation of adherent cell lin... | ["Warm trypsin and RPMI media in a water bath before begining isolation protoccol", "Remove media from cell culture flask and add trypsin. For a small fask (T25) add 3ml of trypsin.", "Place cell flask into the incubator for 5 minutes", "Observe cells under the microscope to check from detachment. Gently tap the side o... |
71,157 | Primary neuron culture for live imaging of axonal cargoes | 1 | dx.doi.org/10.17504/protocols.io.81wgby723vpk/v1 | https://www.protocols.io/view/primary-neuron-culture-for-live-imaging-of-axonal-chqvt5w6 | C. Alexander Boecker, Erika L.F. Holzbaur | TITLE: Primary neuron culture for live imaging of axonal cargoes
AUTHORS: C. Alexander Boecker, Erika L.F. Holzbaur
[DESCRIPTION]
This protocol describes the preparation and culture of mouse primary cortical neurons for live-imaging experiments. Cortices were dissected from mouse embryos at day 15.5. Cortical neurons ... | ["[Day before dissection] Coat glass-bottom imaging dishes with PLL.", "[Day before dissection] Hydrate 100 mg PLL (Sigma) in 50 mL 0.1 Molarity (M) borate buffer, pH 8.5.", "[Day before dissection] Store PLL stock solution (2 mg/mL) in 1 mL aliquots at -80 °C.", "[Day before dissection] On the day before neuron dissec... |
null | null | null | dx.doi.org/10.17504/protocols.io.kg6ctze | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes an optimized protein extraction method for (meta-) proteomic analyses. It is based on several existing protocols (see references below) that were combined and adapted and is also compatible with low biomass samples.</p>
<p> </p>
<p><strong>References: ... | [] |
55,325 | Protocols for eDNA/eRNA extraction from marine samples | 4 | dx.doi.org/10.17504/protocols.io.bz95p986 | https://www.protocols.io/view/protocols-for-edna-erna-extraction-from-marine-sam-bz95p986 | Luca Mirimin, Dulaney Miller, Sara Fernandez | TITLE: Protocols for eDNA/eRNA extraction from marine samples
AUTHORS: Luca Mirimin, Dulaney Miller, Sara Fernandez
[DESCRIPTION]
This document provides a series of protocols used to extract eDNA or eRNA from marine environmental samples such as small and large volume (filtered) water, sediment or (fine mesh net) p... | ["[INTRODUCTION] Note that these nucleic acid extraction protocols have been adapted and tested in conjunction with sampling protocols as detailed in:\n \n\nSee also the relevant peer-reviewed publication here:", "[INTRODUCTION] Overview of protocols included in this document:", "[PROTOCOL 1 - eDNA extraction from wate... |
4,674 | TSS transformation of non-competent E. coli cells | null | dx.doi.org/10.17504/protocols.io.gtabwie | null | Alice Pawlowski | TITLE: TSS transformation of non-competent E. coli cells
AUTHORS: Alice Pawlowski
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Transformation & Storage Solution (2X TSS) enables researchers to take advantage of the simple system described by Chung et al., 1989 (DOI:</span><a href="https://d... | ["[Transformation]\nInoculate 3 ml LB-medium with colonies from a fresh agar plate.", "[Transformation]\nIncubate at 37 °C and 230 rpm for 1.5 to 2.0 h (exponential growth). Culture should become turbid.", "[Transformation]\nMeanwhile prepare 1.5 ml tubes with 200 µl of 2x TSS-buffer and keep on ice. Add 200 µl cells ... |
null | null | null | dx.doi.org/10.17504/protocols.io.kfpctmn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocols describe the steps to perform a western blot in Chlamydomonas reinhardtii cell lysate and supernatant samples.</p>
[BEFORE_START]
<ul>
<li>Check antibody dilutions</li>
<li>Check buffers disponibility</li>
<li>Prepare 5% milk solution</li>
</ul>
[GUIDELINES]
... | [] |
31,497 | Cell Fractionation | null | dx.doi.org/10.17504/protocols.io.bazhif36 | null | Peter Vangheluwe, Sarah Van Veen | TITLE: Cell Fractionation
AUTHORS: Peter Vangheluwe, Sarah Van Veen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Using Ultracentrifugation, this protocol outlines the steps necessary to obtain different organelle fractions from cells. </div></div>
[STEPS] | [] |
62,854 | Standard operating procedures for mosquito vector surveillance, processing and storage | 1 | dx.doi.org/10.17504/protocols.io.eq2lyn13qvx9/v3 | https://www.protocols.io/view/standard-operating-procedures-for-mosquito-vector-b9mer43e | Tanya L Russell, Kyran Staunton, Amanda Murphy, Thomas Burkot | TITLE: Standard operating procedures for mosquito vector surveillance, processing and storage
AUTHORS: Tanya L Russell, Kyran Staunton, Amanda Murphy, Thomas Burkot
[DESCRIPTION]
The purpose of this Standard Operating Procedure (SOP) is to outline processes for the surveillance, processing and storage of mosquito... | ["[Overview of surveillance procedures] Preparation for vector surveillance activities\n· Develop vector surveillance work plan, with required standard operating protocols.\n· Secure the require funding.\n· Gain required research or ethical approvals.\n· Perform a stock-take and then order required equipment and consum... |
81,839 | Generating Ct cut-off values using gBlocks gene fragments | 4 | null | https://www.protocols.io/view/generating-ct-cut-off-values-using-gblocks-gene-fr-ct6pwrdn | Dilip Abraham, Nick Grassly, Catherine Troman, Jonathan Rigby | TITLE: Generating Ct cut-off values using gBlocks gene fragments
AUTHORS: Dilip Abraham, Nick Grassly, Catherine Troman, Jonathan Rigby
[DESCRIPTION]
The following protocol describes the resuspension, dilution, and qPCR of gBlocks gene fragments. gBlocks gene fragments are synthesised double stranded DNA oligos, which... | ["[g-blocks details] gBlocks gene fragments are synthesised double stranded DNA fragments which contain the sequence for the amplicon of interest, in this case for ttr, staG and tviB in S.Typhi, and HF183 bacteroides.", "[Resuspending and diluting the gblocks] gBlocks are supplied as a lyophilised pellet. Resuspend in ... |
54,391 | S. elongatus stock revival | 4 | dx.doi.org/10.17504/protocols.io.bzcxp2xn | https://www.protocols.io/view/s-elongatus-stock-revival-bzcxp2xn | Akashdutta | TITLE: S. elongatus stock revival
AUTHORS: Akashdutta
[DESCRIPTION]
Stocks are more permanent methods of storing bacteria than plates. These stocks can be recovered by pouring them into small volumes of BG-11 and growing under low light levels. As the culture grows, it can be passaged into higher volumes and appropr... | ["Add your stock to 2 mL BG-11 medium in a test tube and grow it overnight.", "Transfer this to a 50 mL flask and make up the culture to 10 mL in volume.", "Once it reaches a lime green colour (#32CD32), add a fresh medium to make the culture up to 50 mL culture in a 150 mL", "Further, make this culture up to 100 mL ... |
15,151 | BG11 medium | null | dx.doi.org/10.17504/protocols.io.s2pegdn | null | Roscoff Culture Collection | TITLE: BG11 medium
AUTHORS: Roscoff Culture Collection
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Medium to grow freshwater cyanobacteria.</div></div>
[STEPS]
?. [Prepare using Sigma Aldrich stock]
Under hood, to 1L of sterile water, add 20 mL of Cyanobacteria BG-11 Freshwater Solution from Si... | ["[Prepare using Sigma Aldrich stock]\nUnder hood, to 1L of sterile water, add 20 mL of Cyanobacteria BG-11 Freshwater Solution from SigmaFilter the medium on 0,2 microns", "[Prepare from base chemicals]\n{\"blocks\":[{\"key\":\"3suc3\",\"text\":\"Stanier RY, Deruelles J, Rippka R, Herdman M, Waterbury JB: Generic Assi... |
35,705 | Viral Titration of SARS-COV-2 by Plaque Assay (Semi-Solid Agarose) | null | dx.doi.org/10.17504/protocols.io.be4zjgx6 | https://www.protocols.io/view/viral-titration-of-sars-cov-2-by-plaque-assay-semi-be4zjgx6 | Björn Meyer | TITLE: Viral Titration of SARS-COV-2 by Plaque Assay (Semi-Solid Agarose)
AUTHORS: Björn Meyer
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol outlines the process of plaque assay for the viral titration of SARS-CoV-2.</div></div>
[STEPS]
?. [Preparing Plaque Overlay (2x)]
Mix with .... | ["[Preparing Plaque Overlay (2x)]\nMix with .\n[MEM]\n[FBS]\nThe final concentration will be 4% in the 2x overlay.", "[Preparing Plaque Overlay (2x)]\nPrewarm the media to .\n37 °C", "[Preparing Plaque Overlay (2x)]\nDissolve in .\n[Agarose]\n[H2O]\nThe final concentration will be 2% in the 2x overlay", "[Preparing P... |
84,190 | E7805 NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina® Protocol for Large Fragment Sizes (> 550 bp) (Chapter 3) | 1 | dx.doi.org/10.17504/protocols.io.rm7vzdy5lx1w/v2 | https://www.protocols.io/view/e7805-nebnext-ultra-ii-fs-dna-library-prep-kit-for-cwf6xbre | New England Biolabs | TITLE: E7805 NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina® Protocol for Large Fragment Sizes (> 550 bp) (Chapter 3)
AUTHORS: New England Biolabs
[DESCRIPTION]
The NEBNext Ultra II FS DNA Library Prep Kit for Illumina contains the enzymes and buffers required to convert a broad range of input amounts of... | ["[Fragmentation/End Prep] Ensure that the Ultra II FS Reaction Buffer is completely thawed. If a precipitate is seen in the buffer, pipette up and down several times to break it up, and quickly vortex to mix. Place on ice until use.", "[Fragmentation/End Prep] Vortex the Ultra II FS Enzyme Mix 5 s - 8 s prior to use a... |
20,520 | U Michigan - Retinal Vascular Permeability | null | dx.doi.org/10.17504/protocols.io.yagfsbw | null | David A. Antonetti | TITLE: U Michigan - Retinal Vascular Permeability
AUTHORS: David A. Antonetti
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">The vascular permeability is quantified by measuring albumin leakage form blood vessels into... | ["Weigh animal and record body weight for anesthetic and dye injections", "Anesthetize animal with ketamine/xylazine mixture", "Make an incision on skin inside of the hind leg and carefully tear away the membranes to isolate the femoral vein", "Inject FITC-BSA into the femoral vein at 2 µl/g body weight (equal to 200 m... |
52,782 | Risk of pregnancy complications in living kidney donors: a meta-analysis | 1 | dx.doi.org/10.17504/protocols.io.bxsnpnde | https://www.protocols.io/view/risk-of-pregnancy-complications-in-living-kidney-d-bxsnpnde | Ioannis Bellos | TITLE: Risk of pregnancy complications in living kidney donors: a meta-analysis
AUTHORS: Ioannis Bellos
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Living kidney donation is growing, especially among young women. However, the risk of subsequent pregnancy complications remain unclear. The present... | ["Objective\n To determine whether living kidney donation is associated with higher risk of developing maternal or fetal complications in subsequent pregnancies.Eligibility criteria\n The rate of pregnancy complications will be compared among women with history of living kidney donation and non-donors. The outcomes of ... |
103,958 | AlphaFold 3 screen | 0 | dx.doi.org/10.17504/protocols.io.6qpvr8rm2lmk/v1 | https://www.protocols.io/view/alphafold-3-screen-dhrw357e | Elias Adriaenssens | TITLE: AlphaFold 3 screen
AUTHORS: Elias Adriaenssens
[DESCRIPTION]
This protocol is about the AlphaFold 3 screen.
[STEPS]
1. Protein sequences were downloaded from the Uniprot server.
2. We accessed AlphaFold 3 from its virtual server (https://alphafoldserver.com) to run pairwise predictions with 5 models per pred... | ["Protein sequences were downloaded from the Uniprot server.", "We accessed AlphaFold 3 from its virtual server (https://alphafoldserver.com) to run pairwise predictions with 5 models per prediction.", "Predictions with an ipTM score of > 0.5 were considered putative hits and diagnostic plots (PAE plot and pLDDT plot) ... |
36,110 | Blunting Protocol for NEB PCR Cloning Kit (E1202) | 1 | dx.doi.org/10.17504/protocols.io.bfhnjj5e | https://www.protocols.io/view/blunting-protocol-for-neb-pcr-cloning-kit-e1202-bfhnjj5e | New England Biolabs | TITLE: Blunting Protocol for NEB PCR Cloning Kit (E1202)
AUTHORS: New England Biolabs
[DESCRIPTION]
This is the blunting protocol for NEB PCR Cloning Kit (E1202).
[BEFORE_START]
Reaction volume may be scaled up or down as necessary.
[GUIDELINES]
Reaction volume may be scaled up or down as necessary.
PCR generat... | ["Mix the following components in a sterile microfuge tube:", "Determine whether your reactions are using DNA digested by restriction enzymes or are sheared/nebulized or PCR products and move forward with the following steps:\n ether you are using", "Immediately inactivate enzyme in the blunting reaction by heating at ... |
null | null | null | dx.doi.org/10.17504/protocols.io.dp85rv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
An LB Agar protocol, adapted from Addgene, to match Northeastern_Boston's protocol.
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
87,105 | Effective Target Capture/Enrichment of Respiratory Viruses from Wastewater | 4 | dx.doi.org/10.17504/protocols.io.8epv5xrjng1b/v1 | https://www.protocols.io/view/effective-target-capture-enrichment-of-respiratory-cza9x2h6 | Lauren Roppolo Brazell, wtaylo, Lolo Aboufoul, Jannatul Ferdous, Aharr206, Jessica A Schlueter, Cynthia Gibas | TITLE: Effective Target Capture/Enrichment of Respiratory Viruses from Wastewater
AUTHORS: Lauren Roppolo Brazell, wtaylo, Lolo Aboufoul, Jannatul Ferdous, Aharr206, Jessica A Schlueter, Cynthia Gibas
[DESCRIPTION]
Human respiratory viruses (HRVs) are highly communicable viral pathogens that present varying degrees of... | ["[Sequence Independent, Single-Primer Amplification [Moreno et al.; 1]] SISPA-A: Reverse Transcription & 2nd Strand cDNA Synthesis", "[Sequence Independent, Single-Primer Amplification [Moreno et al.; 1]] Make a working stock of your SOL Primer A. Stock should be 100 pmol/1μL. Add 4μL of stock + 6μL molecular biology-... |
null | null | null | dx.doi.org/10.17504/protocols.io.h4jb8un | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
43,533 | CeMbio Screen 96WP | 1 | dx.doi.org/10.17504/protocols.io.bnrmmd46 | https://www.protocols.io/view/cembio-screen-96wp-bnrmmd46 | Saul Moore | TITLE: CeMbio Screen 96WP
AUTHORS: Saul Moore
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Protocol for behavioural screening of </span><span style = "font-style:italic;">Caenorhabditis elegans </span><span>response to bacteria from its natural microbiome (CeMbio)</span></div></div>
[STEPS... | ["[Preparing worms]\nUsing an eyebrow hairpick, pick 10 L4-stage N2 worms onto each of 10 OP50-seeded 90mm petri plates 4 days prior to bleaching (e.g. on Monday if bleaching on Friday).", "[Preparing worms]\nOn day of bleaching (e.g. Friday 2pm) follow the protocol for Bleach synchronisation of C. elegans:\n{\"blocks\... |
85,304 | Live-cell imaging for synaptic vesicle precursors in human iNeuron axons | 4 | dx.doi.org/10.17504/protocols.io.5jyl8p9mdg2w/v1 | https://www.protocols.click/view/live-cell-imaging-for-synaptic-vesicle-precursors-cxiyxkfw | Dan Dou, Erika Holzbaur | TITLE: Live-cell imaging for synaptic vesicle precursors in human iNeuron axons
AUTHORS: Dan Dou, Erika Holzbaur
[DESCRIPTION]
Here, we describe procedure and equipment used for live-imaging of synaptic vesicle precursors. This was performed using DIV21 human iPSC-derived excitatory glutamatergic neurons. Equipment an... | ["Image human iNeurons on DIV21, 48-72 hours after transfection with PGK-mScarlet-synaptophysin.", "Replace culture media with low fluorescence imaging media.", "For iNeurons, use Hibernate A medium supplemented with:", "Image using spinning disk confocal microscope under 60x magnification (oil immersion objective). Se... |
51,051 | Low-cost recombinase polymerase amplification (RPA) | 4 | dx.doi.org/10.17504/protocols.io.14egnzryzg5d/v1 | https://www.protocols.io/view/low-cost-recombinase-polymerase-amplification-rpa-bv4jn8un | Smitha Hegde | TITLE: Low-cost recombinase polymerase amplification (RPA)
AUTHORS: Smitha Hegde
[DESCRIPTION]
This protocol describes the expression of enzymes and creation of a master mix for recombinase polymerase amplification (RPA) assays.
[STEPS]
SECTION: Dialysis and protein concentration
4. Dialyse the eluate with it's resp... | ["[Dialysis and protein concentration] Dialyse the eluate with it's respective storage buffer. Follow the video in this link for instructions.\nconcentrate the elaute using a concentrator to required concentration (if your protein working concentration is 600ng/ul, atleast concentrate to 12-20 ug/ul)", "[Column purific... |
51,827 | Viral Tagging and Grow: a scalable approach to capture and characterize infectious virus-host pairs | 4 | dx.doi.org/10.17504/protocols.io.bwutpewn | https://www.protocols.io/view/viral-tagging-and-grow-a-scalable-approach-to-capt-bwutpewn | Ho Bin Jang, Lauren Chittick, Fen Li ., Courtney M Sanderson | TITLE: Viral Tagging and Grow: a scalable approach to capture and characterize infectious virus-host pairs
AUTHORS: Ho Bin Jang, Lauren Chittick, Fen Li ., Courtney M Sanderson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Viral tagging (‘VT’), as shown in the </span><span style = "font-weig... | ["[Amicon tube pre-treatment:]\nPrepare 0.02µm-filtered 1% bovine serum albumin. * The BSA should be freshly prepared (1-2 days, stored at 4°C) before viral washing. *The purpose of this is to better cushion the viruses during the subsequent wash steps and to aid in recovery", "[Amicon tube pre-treatment:]\nWet Amicon ... |
103,084 | Purification of mCherry- or GFP-tagged ATG13/101 subcomplex | 0 | dx.doi.org/10.17504/protocols.io.yxmvmepdng3p/v1 | https://www.protocols.io/view/purification-of-mcherry-or-gfp-tagged-atg13-101-su-dgwk3xcw | Elias Adriaenssens | TITLE: Purification of mCherry- or GFP-tagged ATG13/101 subcomplex
AUTHORS: Elias Adriaenssens
[DESCRIPTION]
This protocol details the purification of mCherry- or GFP-tagged ATG13/101 subcomplex.
[STEPS]
SECTION: Purification - mCherry- or GFP-tagged ATG13/101 subcomplex
1. To purify the mCherry-tagged or GFP-tagged ... | ["[Purification - mCherry- or GFP-tagged ATG13/101 subcomplex] To purify the mCherry-tagged or GFP-tagged ATG13/101 subcomplex, we express mCherry-tagged ATG13 from a pCAG backbone (available from Addgene) together with GST-TEV-ATG101 (available from Addgene) or GST-TEV-GFP-tagged ATG13 from a pCAG backbone (available ... |
90,396 | Rotarod Test | 1 | dx.doi.org/10.17504/protocols.io.bp2l6xrjrlqe/v1 | https://www.protocols.io/view/rotarod-test-c4h4yt8w | Jhodi Webster | TITLE: Rotarod Test
AUTHORS: Jhodi Webster
[DESCRIPTION]
The purpose of this protocol is to assess mice for coordinated movement. Mice who have degeneration within the basal ganglia pathway will display slower movement and fall off the moving rod sooner.
[GUIDELINES]
For analysis:
The numbers you will put into... | ["[PROCEDURE] Turn on rotarod and start up rotarod software.", "[PROCEDURE] Rename the file. I would recommend having a different file name every day you test. This will make analysis easier later.", "[PROCEDURE] Rename the subject names and reset the lanes (on the actual rotarod).", "[PROCEDURE] Set the speed to 4.0 t... |
50,859 | MojoSort™ Whole Blood Human Neutrophil Isolation Kit Protocol | 4 | null | https://www.protocols.io/view/mojosort-whole-blood-human-neutrophil-isolation-ki-bvwjn7cn | Ken Lau | TITLE: MojoSort™ Whole Blood Human Neutrophil Isolation Kit Protocol
AUTHORS: Ken Lau
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol covers usage of BioLegend's MojoSort™ Human Neutrophil Isolation Kit Protocol.</div><div class = "text-block"><span>Please note that BioLegend is no lon... | ["Collect whole blood in collection tube that has anticoagulant, preferably EDTA.Note: Keep MojoSort™ Buffer on ice throughout the procedure.", "Aliquot 1 mL of human whole blood into a 5 mL (12 x 75 mm) polypropylene tube. Add 10 µL of the Biotin-Antibody Cocktail. Mix well and incubate on ice for 15 minutes. Scale up... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.