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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106,456 | Collection and shipment of specimen for single-cell RNA sequencing (scRNA-Seq) | 0 | dx.doi.org/10.17504/protocols.io.kxygxy4b4l8j/v1 | https://www.protocols.io/view/collection-and-shipment-of-specimen-for-single-cel-dj7y4rpw | Laura Robinson, Susan Sheehan, Gaven Garland, Ron Korstanje | TITLE: Collection and shipment of specimen for single-cell RNA sequencing (scRNA-Seq)
AUTHORS: Laura Robinson, Susan Sheehan, Gaven Garland, Ron Korstanje
[DESCRIPTION]
These samples are part of the JAX-Sen project in the SenNet Consortium. Here we provide details on specimen collection and shipment to the Robson labo... | ["[Reagents and Materials:] 2mL Eppendorf tubes or 5 ml Eppendorf tubes\nMACS tissue storage Solution (#130-100-008, MACS Miltenyi Biotech), \ncold storage (4 degrees Celsius)\nTweezers (clean, sterile)", "[Quality Key Points:] The tissue specimen should be kept at 4 degrees Celsius and RNAse-free from its excision unt... |
39,709 | 702.B.3 URMC HTC Lung Tissue Digestion SOP + Worksheet 052820 | 4 | dx.doi.org/10.17504/protocols.io.biz5kf86 | https://www.protocols.io/view/702-b-3-urmc-htc-lung-tissue-digestion-sop-workshe-biz5kf86 | Gloria Pryhuber, Ravi Misra, Tiru Rangasamy, Thomas Mariani, Gautam Bandyopadhyay, Lisa Rogers, Amanda Howell, Claire Wyman, Heidie Huyck, Siva Solleti | TITLE: 702.B.3 URMC HTC Lung Tissue Digestion SOP + Worksheet 052820
AUTHORS: Gloria Pryhuber, Ravi Misra, Tiru Rangasamy, Thomas Mariani, Gautam Bandyopadhyay, Lisa Rogers, Amanda Howell, Claire Wyman, Heidie Huyck, Siva Solleti
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify"... | ["[Procedure]\nRecord details of procedure in the Tables at end of this Worksheet. At HTC, the contents of the Worksheet needs to be transferred to BRINDL Database as soon as possible.", "[Procedure]\nRecord the time the lung tissue was received for dissociation (see Table 1)", "[Procedure]\nWeigh the total lung tissue... |
89,669 | LDW_BDC Muscle scRNAseq | 4 | dx.doi.org/10.17504/protocols.io.ewov1q31ogr2/v1 | https://www.protocols.io/view/ldw-bdc-muscle-scrnaseq-c3tdyni6 | Lauren D Walter, Benjamin D Cosgrove | TITLE: LDW_BDC Muscle scRNAseq
AUTHORS: Lauren D Walter, Benjamin D Cosgrove
[DESCRIPTION]
single-cell RNA sequencing of muscle
[STEPS]
SECTION: Skeletal muscle injury and collection
1. In a given mouse, both tibialis anterior (TA) muscles were injected with 10 µl of notexin (10 µg/ml; Latoxan, France).
13.
SECTION:... | ["[Skeletal muscle injury and collection] In a given mouse, both tibialis anterior (TA) muscles were injected with 10 µl of notexin (10 µg/ml; Latoxan, France).", "[Skeletal muscle injury and collection] The mice were sacrificed, and TA muscles were collected at 0, 1, 2, 3.5, 5, and 7 days post-injury. Each TA was proc... |
59,046 | Expression and purification of recombinant Bsu polymerase | 1 | dx.doi.org/10.17504/protocols.io.x54v9ypkpg3e/v1 | https://www.protocols.io/view/expression-and-purification-of-recombinant-bsu-pol-b5weq7be | lucero.mascaro.r, lucero.merino.c | TITLE: Expression and purification of recombinant Bsu polymerase
AUTHORS: lucero.mascaro.r, lucero.merino.c
[DESCRIPTION]
The DNA polymerase I or Bsu is an enzyme from the Gram (+) bacteria Bacillus subtilis.
The Bsu is used as part of an isothermal DNA amplification based on the recombination process, the RPA react... | ["[DAY1: Transformation of competent cells] Quantify the plasmid containing the Bsu DNA polymerase gene and determine the volume that contains 100 ng of the plasmid.", "[DAY1: Transformation of competent cells] Add the resuspension to an LB agar plate previously supplemented with 0.05 mg/mL and spread the recently tra... |
76,618 | Lignin Reductive Catalytic Fractionation (RCF) Monomers Analysis by Gas Chromatography Flame Ionization Detection (GC-FID) | 6 | dx.doi.org/10.17504/protocols.io.36wgqjerovk5/v1 | https://www.protocols.io/view/lignin-reductive-catalytic-fractionation-rcf-monom-cn3ivgke | Hannah M. Alt, David G. Brandner, Gregg T. Beckham, Kelsey J. Ramirez | TITLE: Lignin Reductive Catalytic Fractionation (RCF) Monomers Analysis by Gas Chromatography Flame Ionization Detection (GC-FID)
AUTHORS: Hannah M. Alt, David G. Brandner, Gregg T. Beckham, Kelsey J. Ramirez
[DESCRIPTION]
A gas chromatography with flame ionization detection (GC-FID) method was developed to quantify r... | ["[Preparation of Standards] By weight, create individual 20,000 µg/mL stock solutions of all monomers (listed in Materials section) and use methanol as the diluent.", "[Preparation of Standards] Combine the stock solutions to create a 1000 µg/mL mixed standard working solution in methanol.", "[Preparation of Standard... |
19,923 | U Mass - Alkaline Phosphatase | null | dx.doi.org/10.17504/protocols.io.xptfmnn | null | Jason Kim | TITLE: U Mass - Alkaline Phosphatase
AUTHORS: Jason Kim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span><span style = "font-weight:bold;"> </span></div><div class = "text-block">
This experiment involves a spectrophotometric measurement using Roche Co... | ["Perform daily quality control assessment of instrumentation before analysis.", "Load each sample into a specialized micro-sample cup for the clinical chemistry\nanalyzer.", "Select Alkaline Phosphatase test on display and run the analysis.", "Collect and analyze the data."] |
46,198 | Evolution of Viral Genomes: Interplay Between Selection, Recombination, and Other Forces | 4 | dx.doi.org/10.17504/protocols.io.brcwm2xe | https://www.protocols.io/view/evolution-of-viral-genomes-interplay-between-selec-brcwm2xe | Stephanie J. Spielman, Steven Weaver, Stephen D. Shank, Brittany Rife Magalis, Michael Li, Sergei L. Kosakovsky Pond | TITLE: Evolution of Viral Genomes: Interplay Between Selection, Recombination, and Other Forces
AUTHORS: Stephanie J. Spielman, Steven Weaver, Stephen D. Shank, Brittany Rife Magalis, Michael Li, Sergei L. Kosakovsky Pond
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Natural selection is a fundame... | ["[3.1 How to Run a Selection Analysis]\nTo execute a selection analysis locally, the following steps will need to be taken:\nThere is a uniform workflow to run any of the described methods, either locally (on one’s own computer and/or a high-performance computing environment) in HyPhy or using the Datamonkey web-servi... |
67,384 | F1 Keto ACV GummiesBurn Calouries Or Gain strength and stamina With This Diet Pills? | 3 | dx.doi.org/10.17504/protocols.io.yxmvmn6dbg3p/v1 | https://www.protocols.io/view/f1-keto-acv-gummiesburn-calouries-or-gain-strength-cd2ys8fw | jasonbalvin | TITLE: F1 Keto ACV GummiesBurn Calouries Or Gain strength and stamina With This Diet Pills?
AUTHORS: jasonbalvin
[DESCRIPTION]
You can skirt the rec center or visit a dietician, simply get our enhancement to find your more youthful rendition and give you helps that no other pill will at any point accomplish for you.... | [] |
90,919 | MBA DToL: DNA barcoding of macroalgae and microalgae, marine fungi and lichens | 1 | null | https://www.protocols.io/view/mba-dtol-dna-barcoding-of-macroalgae-and-microalga-c42fyybn | Rebekka Uhl, Joanna Harley, Helen Jenkins, Susan Wharam | TITLE: MBA DToL: DNA barcoding of macroalgae and microalgae, marine fungi and lichens
AUTHORS: Rebekka Uhl, Joanna Harley, Helen Jenkins, Susan Wharam
[DESCRIPTION]
Version 1.5
Purpose: This SOP outlines the method used to DNA barcode macroalgae and marine protists (microalgae), fungi and lichens for the DToL projec... | ["Sequence generation\nNote: the method has evolved during the project, and has therefore varied between\nsamples. Initially, DNA was extracted from samples prior to PCR. Later,\ntissue-direct, Phire PCR was used to improve throughput and potentially lessen\nthe impacts of inhibiters in samples. Both methods generate r... |
null | null | null | dx.doi.org/10.17504/protocols.io.idcca2w | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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48,289 | Timing ofinitial discussions of advance care planning among patients on maintenance dialysis: A protocol for cross-sectional study | 1 | dx.doi.org/10.17504/protocols.io.btd9ni96 | https://www.protocols.io/view/timing-ofinitial-discussions-of-advance-care-plann-btd9ni96 | Yasushi Tsujimoto | TITLE: Timing ofinitial discussions of advance care planning among patients on maintenance dialysis: A protocol for cross-sectional study
AUTHORS: Yasushi Tsujimoto
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">MAIN PROTOCOL</div></div>
[STEPS]
?. Timing ofinitial discussions of advance care plan... | ["Timing ofinitial discussions of advance care planning among patients on maintenance dialysis: A protocol for cross-sectional study\n\t\t\t\t\t\t\t .justify:after {\n\t\t\t\t\t\t\t content: \"\";\n\t\t\t\t\t\t\t display:inline-block;\n\t\t\t\t\t\t\t width: 100%;\n\t\t\t\t\t\t\t }\n\t\t\t\t\t\t\t\n\t\t\t\t\t... |
36,584 | Phosphate Buffer | null | dx.doi.org/10.17504/protocols.io.bfygjptw | https://www.protocols.io/view/phosphate-buffer-bfygjptw | Neilier Junior | TITLE: Phosphate Buffer
AUTHORS: Neilier Junior
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A buffer solution has the function of resisting changes in pH even when adding powerful acids or bases. However, in the physiological environment the buffered system also provides cofactors for enzymatic ... | ["[Phosphate Buffer]\nMix sodium phosphate monobasic and dibasic solutions in the proportions indicated. ABCDEFGHIJKL1mL of Sodium phosphate, Monobasic92.081.573.562.551 .039.028.019.013.08.55.32mL of Sodium phosphate, Dibasic8.018.526.537.549.061 .072.081.087.091.594.73pH5.86.26.46.66.87.07.27.47.67.88.0\npH range: ... |
43,794 | In-house automated Smart-Seq2 | 1 | dx.doi.org/10.17504/protocols.io.bnzsmf6e | https://www.protocols.io/view/in-house-automated-smart-seq2-bnzsmf6e | Lira Mamanova | TITLE: In-house automated Smart-Seq2
AUTHORS: Lira Mamanova
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This SOP describes the procedure for the in-house automated Smart-Seq2 workflow with off-the-shelf reagents. This set up utilises the benchtop robots and significantly reduces the experimental... | ["[Preparation of lysis buffer plates and single-cell samples]\nFor each well, prepare the Triton buffer by adding of RNAse inhibitor and of diluted (1/500,000) ERCCs to the of Triton X-100. Prepare an RLT lysis buffer by using of RLT buffer (Qiagen); of DTT (2M) and of diluted (1/500,000) ERCCs. Dispense of Tr... |
62,124 | Ugly CBD Gummies Is It Fake Or Trusted | 3 | dx.doi.org/10.17504/protocols.io.bp2l6135rvqe/v1 | https://www.protocols.io/view/ugly-cbd-gummies-is-it-fake-or-trusted-b8wkrxcw | purecbdsale CBD | TITLE: Ugly CBD Gummies Is It Fake Or Trusted
AUTHORS: purecbdsale CBD
[DESCRIPTION]
https://www.24x7supplement.com/Ugly-CBD-Gummie/
[STEPS] | [] |
70,907 | Plasmid transduction using competent cell | 4 | dx.doi.org/10.17504/protocols.io.j8nlkw4e5l5r/v2 | https://www.protocols.io/view/plasmid-transduction-using-competent-cell-chg3t3yn | An.Huang | TITLE: Plasmid transduction using competent cell
AUTHORS: An.Huang
[DESCRIPTION]
Plasmid can be transduced into bacteria at competent state using heat shock. This protocol helps transduce plasmid into competent cells.
[STEPS]
1. Take competent cell out from -80℃ fridge and thaw on ice.
2. When the cells are completel... | ["Take competent cell out from -80℃ fridge and thaw on ice.", "When the cells are completely thawed, pipette 2 µL plasmid DNA solution into 100 µL competent cell.\nPut the cell in ice for 30 min", "Conduct heat shock on the competent cell by placing the cell in 42 °C water bath for 90 s.\nPut the cells back into ice fo... |
66,460 | Expression and purification Twin-STREP-FLAG tagged ATG13:ATG101 constructs | 4 | dx.doi.org/10.17504/protocols.io.yxmvmn4yng3p/v1 | https://www.protocols.io/view/expression-and-purification-twin-strep-flag-tagged-cc54sy8w | Adam Yokom, Xuefeng Ren | TITLE: Expression and purification Twin-STREP-FLAG tagged ATG13:ATG101 constructs
AUTHORS: Adam Yokom, Xuefeng Ren
[DESCRIPTION]
Expression and purification Twin-STREP-FLAG tagged ATG13:ATG101 constructs
[STEPS]
SECTION: Expression
1. Transfect HEK GNTI cells at concentration of 2 × 106 cells/ml
SECTION: Puri... | ["[Expression] Transfect HEK GNTI cells at concentration of 2 × 106 cells/ml", "[Purification] Resuspended pellet in lysis buffer (25 mM HEPES pH 7.5, 200 mM NaCl, 2 mM MgCl2, 1 mM TCEP, 5 mM EDTA, 10% Glycerol) with 1% Triton X-100 and protease inhibitor cocktail (Thermo Scientific, Waltham, MA) for 15 min", "[Express... |
108,352 | Preparation of Linked-Read Sequencing Libraries using Haplotagging beads | 0 | dx.doi.org/10.17504/protocols.io.5jyl827m8l2w/v1 | https://www.protocols.io/view/preparation-of-linked-read-sequencing-libraries-us-dm2848hw | marek.kucka, Yingguang Frank Chan | TITLE: Preparation of Linked-Read Sequencing Libraries using Haplotagging beads
AUTHORS: marek.kucka, Yingguang Frank Chan
[DESCRIPTION]
Description:
Haplotagging beads are prepared in form of a 96 well plate where each well contains M280-Streptavidin beads linked with complete and barcoded i5 and i7 Tn5-sequencing ad... | ["[Linked-read library preparation from High molecular gDNA] Dilute gDNA of each sample to 0.15 ng DNA/ul in 10mM Tris, pH=8\nCheck with HS Qubit concentration of your diluted gDNA using 10 (1.5ng) or 20 (3ng) ul of diluted 0.15ng/ul gDNA", "[Linked-read library preparation from High molecular gDNA] Aliquot 1 U of Hapl... |
null | null | null | dx.doi.org/10.17504/protocols.io.dm849v | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
The NEXTflex™ Rapid Directional qRNA-Seq Kit is designed to prepare directional, strandspecific RNA libraries for sequencing using Illumina® sequencers while enabling the high precision measurement of RNA molecules. <br /><br />Please see the <a href="http://www.b... | [] |
69,848 | Quantitative analyses of the ultrastructural features of dopaminergic axon terminals | 2 | dx.doi.org/10.17504/protocols.io.bp2l694xdlqe/v1 | https://www.protocols.io/view/quantitative-analyses-of-the-ultrastructural-featu-cgfyttpw | Natalie M Doig, Peter J Magill | TITLE: Quantitative analyses of the ultrastructural features of dopaminergic axon terminals
AUTHORS: Natalie M Doig, Peter J Magill
[DESCRIPTION]
The release of dopamine from axons is critical for normative brain function and behaviour. Impaired or otherwise inappropriate dopamine release often correlates with changes... | [] |
103,304 | Soil eDNA Sample Collection Protocol | 4 | null | https://www.protocols.io/view/soil-edna-sample-collection-protocol-dg5g3y3w | Stephen Douglas Russell | TITLE: Soil eDNA Sample Collection Protocol
AUTHORS: Stephen Douglas Russell
[DESCRIPTION]
**This protocol represents an initial working draft for community-science-based collection and processing of soil samples for eventual eDNA analysis. This notice will be removed once the protocol has been fully tested and revise... | ["[Ordering the kit] This protocol requires that you have a Soil eDNA Sample Collection Kit from Mycota Lab. They can be ordered online here:\n\nhttp://www.mycota.com/shop (in the future)\n\nBefore ordering the kit, be sure your intended sampling location is not within one of the USDA's APHIS Quarantine Areas. We are n... |
51,028 | Whole Cell Patch Clamp of Dispersed Human Islet Cells | 4 | dx.doi.org/10.17504/protocols.io.bv3un8nw | https://www.protocols.io/view/whole-cell-patch-clamp-of-dispersed-human-islet-ce-bv3un8nw | Xiaoqing Dai, Austin Bautista, Patrick E Macdonald | TITLE: Whole Cell Patch Clamp of Dispersed Human Islet Cells
AUTHORS: Xiaoqing Dai, Austin Bautista, Patrick E Macdonald
[DESCRIPTION]
Cells use exocytosis to secrete a wide variety of molecules, including proteins, hormones, and neurotransmitters. Exocytosis can be monitored at the single-cell level by using patch-c... | ["[Procedure] On the day receiving the shipped human pancreatic islets, hand-picked islets are dissociated to single cells using StemPro accutase (Gibco/Fisher, A11105-01). Plate cells in cell culture dishes, and culture in DMEM with 5.5 mM glucose, 10% FBS, and 100 U/mL penicillin/ streptomycin for 1-4 days.", "[Pro... |
103,201 | Immunostaining of Human Frontal Cortex Sections | 0 | dx.doi.org/10.17504/protocols.io.j8nlk8mk5l5r/v1 | https://www.protocols.io/view/immunostaining-of-human-frontal-cortex-sections-dgz93x96 | Shiyi Wang | TITLE: Immunostaining of Human Frontal Cortex Sections
AUTHORS: Shiyi Wang
[DESCRIPTION]
Immunostaining of Human Frontal Cortex Sections
[STEPS]
1. **Tissue Acquisition**
1.1. - Obtain 40 μm thick floating sections of human frontal cortex from Banner Sun Health Research Institute in Sun City, Arizona.
1.2. - Use sect... | ["**Tissue Acquisition**", "- Obtain 40 μm thick floating sections of human frontal cortex from Banner Sun Health Research Institute in Sun City, Arizona.", "- Use sections from 4 control subjects and 3 LRRK2 G2019S mutation carrier subjects.", "**Subject Information**", "- Verify that control subjects had no history o... |
97,833 | Tail Suspension Test | 1 | dx.doi.org/10.17504/protocols.io.6qpvr3222vmk/v2 | https://www.protocols.io/view/tail-suspension-test-dbsh2nb6 | Marina Lorente Picón, Núria Peñuelas, Ariadna Laguna, Marta Gonzalez-Sepulveda, Miquel Vila | TITLE: Tail Suspension Test
AUTHORS: Marina Lorente Picón, Núria Peñuelas, Ariadna Laguna, Marta Gonzalez-Sepulveda, Miquel Vila
[DESCRIPTION]
Tail Suspension Test for mice
[STEPS]
1. Suspend animals by their tails with tape in a suspension bar.
2. To avoid the tail climbing behavior, pass a 2cm methacrylate tube thr... | ["Suspend animals by their tails with tape in a suspension bar.", "To avoid the tail climbing behavior, pass a 2cm methacrylate tube through the tail before suspending the animal.", "Quantify the escape-oriented behaviors (i.e. fore and hind limbs movement) during six minutes. Vocalizations were registered during this ... |
51,081 | Run ReVisE from Docker | 5 | dx.doi.org/10.17504/protocols.io.bv5hn836 | https://www.protocols.io/view/run-revise-from-docker-bv5hn836 | Alexey Kuzin, Stepan Orlov, Егор Усик, Alexey Zhuravlev | TITLE: Run ReVisE from Docker
AUTHORS: Alexey Kuzin, Stepan Orlov, Егор Усик, Alexey Zhuravlev
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes run of ReVisE server from Docker container on Ubuntu. It describes retrieving of the Docker and the container only. It refers ... | ["[Docker installation]\nThe machine where ReVisE server is to be run must have Docker Engine installed. One can install Docker Engine according to this reference. Or install Docker Community Edition (CE) according to the next sub-steps:", "[Docker installation]\nRemove old Docker packages, if they present:sudo apt rem... |
80,821 | Geographic Information Systems (GIS)-based spatial analysis of cell distribution | 1 | dx.doi.org/10.17504/protocols.io.ewov1o697lr2/v1 | https://www.protocols.io/view/geographic-information-systems-gis-based-spatial-a-cs6vwhe6 | Adalberto Merighi, Laura Lossi | TITLE: Geographic Information Systems (GIS)-based spatial analysis of cell distribution
AUTHORS: Adalberto Merighi, Laura Lossi
[DESCRIPTION]
This protocol describes how to perform a Geographic Information Systems (GIS)-based spatial analysis of cerebellar images. It can be used for any biological images to study cell... | ["[Calculation of cells' X-Y coordinates]", "[Calculation of cells' X-Y coordinates] Open the image to be analyzed using Fiji: File → Open", "[Calculation of cells' X-Y coordinates] Set the appropriate scale for the image using Analyze → Set Scale. In the pop-up window report the distance in pixels relat... |
null | null | null | dx.doi.org/10.17504/protocols.io.j4mcqu6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Here we describe two methods for assessing the ability of one bacteria to inhibit the growth of another through the production of antimicrobial compounds. In the first assay, the double agar layer method, only the secreted substances but not the candidate antagonist bacteria ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.e8dbhs6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a collection of G-Biosciences protocols using XIT™ Genomic DNA Blood Kit for the isolation of genomic DNA from fresh blood, bone marrow & buffy coat.</p>
[STEPS]
?. | [] |
51,766 | Preparation of fibrils and Quality control | 1 | dx.doi.org/10.17504/protocols.io.bwswpefe | https://www.protocols.io/view/preparation-of-fibrils-and-quality-control-bwswpefe | The Michael J Fox Foundation Pff Standardization Consortium | TITLE: Preparation of fibrils and Quality control
AUTHORS: The Michael J Fox Foundation Pff Standardization Consortium
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a consensus protocol developed through discussions with Laura Volpicelli-Daley, Caryl Sortwell, Kelvin Luk, Lindsey Gottler, ... | ["[Step 1. Preparation of fibrils. (Timing ~30 min; 7 days for fibril formation)]\nThaw aliquot of “Alpha-Synuclein Monomer Protein for Making PreFormed Fibrils” or other recombinant aSyn monomer .\non ice", "[Step 1. Preparation of fibrils. (Timing ~30 min; 7 days for fibril formation)]\nCentrifuge at for in benchto... |
61,917 | Peptide-MHC Dextramer Assembly | 1 | dx.doi.org/10.17504/protocols.io.3byl4b33ovo5/v1 | https://www.protocols.io/view/peptide-mhc-dextramer-assembly-b8p5rvq6 | Zaki Molvi | TITLE: Peptide-MHC Dextramer Assembly
AUTHORS: Zaki Molvi
[DESCRIPTION]
This protocol details the assembly of peptide-MHC dextramers for use in downstream applications, including flow cytometric detection or magnetic enrichment of T cells specific for a given peptide-MHC (pMHC). Dextramer assembly of biotinylated pMH... | ["[Introduction] This protocol details the assembly of peptide-MHC dextramers for use in flow cytometric detection or magnetic enrichment of T cells specific for a given peptide-MHC (pMHC). pMHC are generated via UV-exchange and multimerized onto a dextran backbone, which can be functionalized with any fluorophore-conj... |
79,033 | EdU Immunohistochemistry using Click-it reaction | 4 | null | https://www.protocols.io/view/edu-immunohistochemistry-using-click-it-reaction-crezv3f6 | Anita Gola | TITLE: EdU Immunohistochemistry using Click-it reaction
AUTHORS: Anita Gola
[DESCRIPTION]
This protocol allows users to image histology tissue using basic immunohistochemistry techniques in combination with EdU capture (using the Click-it reaction system). EdU (5-ethynyl-2′-deoxyuridine) will capture S-phase cells w... | ["[Tissue Preparation and Sectioning] Inject animals with EdU as outlined in animal protocol license (typically by performing an intra-peritoneal injection with 200 mg/kg per mouse).", "[Tissue Preparation and Sectioning] Euthanize animal and harvest organ of interest: place tissue in 0.1% BD cytofix/cytoperm fixative ... |
100,125 | Nuclei isolation, immunostaining, and Fluorescence-activated nuclei sorting (FANS) for Smart-Seq2 | 0 | dx.doi.org/10.17504/protocols.io.j8nlk8wjxl5r/v1 | https://www.protocols.io/view/nuclei-isolation-immunostaining-and-fluorescence-a-ddz52786 | Ester Kalef-Ezra, Dominic Horner, George Morrow, Vanda Knitlhoffer, Andy Goldson, Iain Macaulay, Yanping Guo, Christos Proukakis | TITLE: Nuclei isolation, immunostaining, and Fluorescence-activated nuclei sorting (FANS) for Smart-Seq2
AUTHORS: Ester Kalef-Ezra, Dominic Horner, George Morrow, Vanda Knitlhoffer, Andy Goldson, Iain Macaulay, Yanping Guo, Christos Proukakis
[DESCRIPTION]
This protocol describes the steps for extracting nuclei from h... | ["[Nuclei isolation from human post-mortem brain tissue] Preparation:\n\nUV-treat 96-well plates prior to use.", "[Nuclei isolation from human post-mortem brain tissue] Pre-weight tubes are needed for tissue scaling.", "[Nuclei isolation from human post-mortem brain tissue] Clean pestles the day before with 0.2 Molarit... |
83,205 | Preparation and cryopreservation of human liver samples for analysis by flow cytometry (fresh or after cryobanking) | 1 | dx.doi.org/10.17504/protocols.io.8epv5x7e4g1b/v1 | https://www.protocols.io/view/preparation-and-cryopreservation-of-human-liver-sa-cvhdw326 | Wiebke Werner, Linda Hammerich | TITLE: Preparation and cryopreservation of human liver samples for analysis by flow cytometry (fresh or after cryobanking)
AUTHORS: Wiebke Werner, Linda Hammerich
[DESCRIPTION]
This protocol focuses on the preparation of small human liver samples for single-cell analysis by flow cytometry. It provides two options for... | ["[Preparations (before samples are aquired from the OR)] Start the biosafety cabinet.", "[Preparations (before samples are aquired from the OR)] Prepare all the reagents and equipment needed for cell isolation.", "[Preparations (before samples are aquired from the OR)] Place all needed buffers and reagents, including ... |
23,750 | Conscious Cystometry Bladder Function Testing | null | dx.doi.org/10.17504/protocols.io.3fegjje | null | Firouz Daneshgari | TITLE: Conscious Cystometry Bladder Function Testing
AUTHORS: Firouz Daneshgari
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Cystometry is a test of bladder function in which pressure and volume of fluid in the blad... | ["Use scissors to cut the sealed tube located between the animal’s ears.", "Attach the end of the tube not connected to the metabolic cage swivel device to the tube between the animal’s ears.", "Start the saline syringed filled pump (Kent Scientific Corporation, Torrington, CT, USA) to flush debris within the animal’s ... |
21,226 | Vandy - Mouse Echocardiography | null | dx.doi.org/10.17504/protocols.io.yyifxue | null | Chee Lim | TITLE: Vandy - Mouse Echocardiography
AUTHORS: Chee Lim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">Transthoracic mouse echocardiography is used to provide noninvasive imaging of the heart and allows for quantificat... | ["The chest hair is first shaved and a topical delipatory agent (e.g. Nair) is used to remove any remaining body hair.", "The conscious mouse is held in the prone position, decreasing vagal reflexes and associated abnormalities of heartrate or AV conduction. If anesthesia is required, 3% isoflurane is used for... |
69,552 | Fluo-3-AM Assay | 1 | null | https://www.protocols.io/view/fluo-3-am-assay-cf6qtrdw | Thermo Fisher | TITLE: Fluo-3-AM Assay
AUTHORS: Thermo Fisher
[DESCRIPTION]
determine the intracellular Ca2+ concentration of your cells via a fluorescence marker
[STEPS]
1. dilute the DMSO stock solution (1-5mM) to 1-5μM in the buffered physiological medium of choice
2. Pluronic F-127 may be added to a concentration of 0.02 % volum... | ["dilute the DMSO stock solution (1-5mM) to 1-5μM in the buffered physiological medium of choice", "Pluronic F-127 may be added to a concentration of 0.02 % volume", "incubate an aliquot of the cells with Fluo-3-AM for 60 min at 20 °C -37 °C", "wash the cells in indicator-free medium and incubate the cells for another... |
78,248 | Protocol: HLA and Nasal Polyposis susceptibility: A meta-analysis of worldwide studies | 1 | dx.doi.org/10.17504/protocols.io.bp2l69y5dlqe/v1 | https://www.protocols.io/view/protocol-hla-and-nasal-polyposis-susceptibility-a-cqngvvbw | Ryan Witcher, anursu, grube.jordon | TITLE: Protocol: HLA and Nasal Polyposis susceptibility: A meta-analysis of worldwide studies
AUTHORS: Ryan Witcher, anursu, grube.jordon
[DESCRIPTION]
Nasal polyposis (NP) is a common and recurrent condition of the upper respiratory tract that can lead to significant morbidity. NP are noncancerous growths that develo... | ["[Administrative Information] Title\nProtocol: HLA and Nasal Polyposis susceptibility: A meta-analysis of worldwide studies", "[Administrative Information] Registration \nRegistration is via protocols.io", "[Administrative Information] Authors\nRyan A. Witcher, BS: Lake Erie College of Osteopathic Medicine- Bradenton,... |
36,814 | Modified protocol for URA3 counter-selection at highly expressed regions of Saccharomyces cerevisiae | null | dx.doi.org/10.17504/protocols.io.bf7njrme | https://www.protocols.io/view/modified-protocol-for-ura3-counter-selection-at-hi-bf7njrme | Lenny Teytelman, Jasper Rine | TITLE: Modified protocol for URA3 counter-selection at highly expressed regions of Saccharomyces cerevisiae
AUTHORS: Lenny Teytelman, Jasper Rine
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This is a modified protocol for </span><span style = "font-style:italic;">URA3 </span><span>counter-... | ["[Transformation and selection]\nPerform the standard LiAc transformation to replace the locus of interest with the URA3 cassette.", "[Transformation and selection]\nGrow on CSM-Ura3 plates and confirm that the integration is correct by sequencing.", "[Counter-selection against URA3]\nPerform the standard LiAc transfo... |
null | null | null | dx.doi.org/10.17504/protocols.io.hisb4ee | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol describes steps and considerations for working in the field to collect samples to be used for molecular work targetting marine (or freshwater) microbial eukaryotes. See downstream protocols for <a href="https://www.protocols.io/view/RNA-and-optional-DNA-extracti... | [] |
66,301 | Recrutamento das voluntárias | 1 | dx.doi.org/10.17504/protocols.io.j8nlkkje6l5r/v1 | https://www.protocols.io/view/recrutamento-das-volunt-rias-ccy5sxy6 | Alicia Rafaelly Vilefort Sales, Daniel Vartanian, Maria Augusta Medeiros Andrade | TITLE: Recrutamento das voluntárias
AUTHORS: Alicia Rafaelly Vilefort Sales, Daniel Vartanian, Maria Augusta Medeiros Andrade
[DESCRIPTION]
Este protocolo foi desenhado para o processo de coleta de dados do projeto de pesquisa Sono e Gravidez. Consulte a aba Guidelines para visualizar o fluxograma do processo como um ... | ["[Abordagem] Apresente o projeto à voluntária.", "[Abordagem] Peça para a voluntária ler com atenção o Termo de Consentimento Livre e Esclarecido (TCLE) e preencher e assinar todos os campos indicados.", "[Abordagem] Peça para a voluntária responder o formulário de campo.\n\nSiga para o próximo passo enquanto a gestan... |
69,823 | Quick DNA Extraction for Fungal Barcoding (X-Amp) | 4 | dx.doi.org/10.17504/protocols.io.4r3l2oy2pv1y/v3 | https://www.protocols.io/view/quick-dna-extraction-for-fungal-barcoding-x-amp-cge7tthn | Stephen Douglas Russell | TITLE: Quick DNA Extraction for Fungal Barcoding (X-Amp)
AUTHORS: Stephen Douglas Russell
[DESCRIPTION]
Below you will find a simple and fast two-step DNA extraction protocol that works well with many different groups of fungi. This protocol can be utilized in preparation for DNA barcoding of fungi utilizing Oxf... | ["[Initial Preparation] Begin by laying out (96) 0.2mL cells on a 96-well PCR plate rack. This can be done in a plate or strip format. \n\nEven though it costs more, I prefer to use 8-strips with individual caps as they are easier to work with. Only a single sample cell needs to be open at a time, individual rows can b... |
45,350 | SDS-PAGE gel electrophoresis | 4 | null | https://www.protocols.io/view/sds-page-gel-electrophoresis-bqiemube | Steven Burgess | TITLE: SDS-PAGE gel electrophoresis
AUTHORS: Steven Burgess
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">SDS-PAGE gel electrophoresis protocol for analyzing samples from plant leaf tissue via immunofluorescence. In this protocol no Coomassie blue is added to samples, the reason is that this inter... | ["[Prepare gel tank and buffers]\nCreate a working dilution of Tris-Glycine running buffer (~ is required per gel tank) by diluting 1:10 with d H2O.\n1 L", "[Prepare gel tank and buffers]\nCarefully remove the comb from the precast gel and the tape across the bottom.", "[Prepare gel tank and buffers]\nAssemble the Min... |
null | null | null | dx.doi.org/10.17504/protocols.io.c4bysm | null | null | TITLE: No Title
AUTHORS:
[BEFORE_START]
Prepare lysis buffer as described in guidelines.
[GUIDELINES]
2.0 mL Lysis Buffer is added to Sterivex immediately after filtration. Filters are stored at -20°C or -80°C.<br /><br />Lysis Buffer is: <br /><br />
<table>
<tbody>
<tr>
<td>Final Concentration</... | [] |
91,656 | Visium Direct Mount FFPE -- University of Minnesota TMCs | 1 | dx.doi.org/10.17504/protocols.io.kxygx3qpkg8j/v1 | https://www.protocols.io/view/visium-direct-mount-ffpe-university-of-minnesota-t-c5rgy53w | Laura J Niedernhofer, David A Bernlohr | TITLE: Visium Direct Mount FFPE -- University of Minnesota TMCs
AUTHORS: Laura J Niedernhofer, David A Bernlohr
[DESCRIPTION]
The Visium Spatial Gene Expression for FFPE is designed to measure mRNA in tissue sections derived
from formalin fixed & paraffin embedded (FFPE) tissue samples and requires a Visium Spatial sl... | ["[Deparaffinization, H&E Staining, Imaging & Decrosslinking]", "[Library Preparation & Sequencing]", "[FASTQ Generation] BCL data from Illumina sequencer is demultiplexed and converted into FASTQ format using bcl2fastq software version 2.20.0"] |
29,877 | Does CSR Affect the Cost of Equity Capital? -- Empirical Evidence from Targeted Poverty Alleviation of Listed Companies in China | null | dx.doi.org/10.17504/protocols.io.9evh3e6 | null | Yuting Yi | TITLE: Does CSR Affect the Cost of Equity Capital? -- Empirical Evidence from Targeted Poverty Alleviation of Listed Companies in China
AUTHORS: Yuting Yi
[STEPS]
?. | [] |
59,517 | cDNA library preparation using ARTIC v3 primers and NEB UDI UMI adaptors for NGS | 4 | dx.doi.org/10.17504/protocols.io.3byl4b99ovo5/v1 | https://www.protocols.io/view/cdna-library-preparation-using-artic-v3-primers-an-b6c5ray6 | Trevor Ho, Nahuel Manzanaro Moreno, Marion Walker, Nick Gilbert, Livia C T Scorza | TITLE: cDNA library preparation using ARTIC v3 primers and NEB UDI UMI adaptors for NGS
AUTHORS: Trevor Ho, Nahuel Manzanaro Moreno, Marion Walker, Nick Gilbert, Livia C T Scorza
[DESCRIPTION]
This is a cDNA library preparation protocol with the aim to quantify SARS-CoV-2 in wastewater and potentially detect its diffe... | ["[cDNA synthesis] For cDNA synthesis, refer to \n\nNEBNext® ARTIC SARS-CoV-2 Library Prep Kit (Illumina®) NEB #E7650S/L \n\nChapter 2 Standard Protocol with cDNA Amplicon and Ligation Bead Cleanups (Three clean-up steps)\n\n- Follow steps 2.1 to 2.3", "[Ligate amplified cDNA to NEB UDI UMI adaptors] For choosing ada... |
32,639 | Defined Media Primary Mouse Hippocampal Neuron Culture | null | dx.doi.org/10.17504/protocols.io.bb47iqzn | null | Kristopher Plambeck | TITLE: Defined Media Primary Mouse Hippocampal Neuron Culture
AUTHORS: Kristopher Plambeck
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Culture of primary mouse hippocampal neurons. This protocol is for a defined media culture, meaning the use of a feeder layer is not required.</div></div>
[STE... | ["Wash coverslips 3x with distilled water and place wax dots on coverslips", "a.Transfer coverslips to 6-well plates (at least four; 24 coverslips total) in biosafety cabinet.", "b.For sterility, turn on bunsen burner and place near hot plate.Sterilize bench area with 70% ethanol.", "c.Begin boiling water in small beak... |
null | null | null | dx.doi.org/10.17504/protocols.io.f5hbq36 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol for RNA Purification form Plasma or Serum, using the ISOLATE II Biofluids RNA Kit. This protocol includes the lysate preparation procedure.</p>
[BEFORE_START]
<div class="page" title="Page 17">
<div class="section">
<div class="layoutArea">
<div class="column">
<p> ... | [] |
91,865 | Bulk RNAseq - Mouse Adipose Tissue - University of Minnesota TMCs | 1 | dx.doi.org/10.17504/protocols.io.3byl4q138vo5/v1 | https://www.protocols.io/view/bulk-rnaseq-mouse-adipose-tissue-university-of-min-c5xzy7p6 | Laura J Niedernhofer, David A Bernlohr | TITLE: Bulk RNAseq - Mouse Adipose Tissue - University of Minnesota TMCs
AUTHORS: Laura J Niedernhofer, David A Bernlohr
[DESCRIPTION]
Bulk RNA sequencing is the method of choice for transcriptomic analysis of pooled cell populations, tissue sections, or biopsies. It measures the average expression level of individual... | ["[RNA Isolation (from Thermo Fisher TRIzolReagent User Guide)] Lyse and homogenize samples in TRIzol Reagent according to the starting material (adipose tissue). \nAdd 1 mL of TRIzol Reagent per 50-100 mg of tissue to the sample and homogenize using a homogenizer.", "[RNA Sequencing] Cluster generation and sequencing:... |
41,137 | ELISA for quantification of IL-1 in human serum or plasma. | 6 | dx.doi.org/10.17504/protocols.io.bkerktd6 | https://www.protocols.io/view/elisa-for-quantification-of-il-1-in-human-serum-o-bkerktd6 | Angel Justiz-Vaillant | TITLE: ELISA for quantification of IL-1 in human serum or plasma.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other b... | ["An anti-human IL-1 coating antibody is adsorbed onto microwells by incubation overnight at 4°C.", "Add 50 µl of human serum. Human IL-1 present in the serum sample binds to antibodies adsorbed to the microwells.", "The microplate is blocked with 3% non-fat milk-PBS buffer and later wasth o remove unbound proteins.",... |
105,905 | Lentivirus Production | 4 | dx.doi.org/10.17504/protocols.io.8epv5ro85g1b/v1 | https://www.protocols.io/view/lentivirus-production-djnr4md6 | Anita Adami | TITLE: Lentivirus Production
AUTHORS: Anita Adami
[DESCRIPTION]
This protocol is about the production of lentivirus.
[STEPS]
SECTION: PEI stock solution preperation
1. Dissolve Polyethyleneimine [Polysciences PN 23966] by swirling using de-ionized H2O heated to 80 °C and using ~90% of volume required to reach a fin... | ["[PEI stock solution preperation] Dissolve Polyethyleneimine [Polysciences PN 23966] by swirling using de-ionized H2O heated to 80 °C and using ~90% of volume required to reach a final concentration of 1 1501 [1 μg/μl].", "[PEI stock solution preperation] Cool to Room temperature.", "[PEI stock solution preperation]... |
73,908 | ONT V14 Nanopore Adapter Ligation for Fungal DNA Barcoding | 4 | dx.doi.org/10.17504/protocols.io.dm6gpb5zdlzp/v4 | https://www.protocols.io/view/ont-v14-nanopore-adapter-ligation-for-fungal-dna-b-ckeuutew | Stephen Douglas Russell | TITLE: ONT V14 Nanopore Adapter Ligation for Fungal DNA Barcoding
AUTHORS: Stephen Douglas Russell
[DESCRIPTION]
This process will take your A-tailed library and add the nanopore adapters. Simply combine several chemicals for a single reaction and do a bead cleanup.
Tested with:
Flowcells: Flongle 10.4.1 or Min... | ["[Adapter Ligation] Spin down the Ligation Adapter (LA) and Quick T4 Ligase, and place on ice.\n\nLA - \nQuick T4 Ligase -", "[Adapter Ligation] Thaw Ligation Buffer (LNB) at room temperature, spin down and mix by pipetting. Due to viscosity, vortexing this buffer is ineffective. Place on ice immediately after thawi... |
62,972 | XR Massive Male Enhancement (Scam Pills Or Legit) Full Detailed Review! | 3 | dx.doi.org/10.17504/protocols.io.bp2l61m25vqe/v1 | https://www.protocols.io/view/xr-massive-male-enhancement-scam-pills-or-legit-fu-b9q4r5yw | XR Massive Male Enhancement | TITLE: XR Massive Male Enhancement (Scam Pills Or Legit) Full Detailed Review!
AUTHORS: XR Massive Male Enhancement
[DESCRIPTION]
MUST CHECK: *Special Discounted Pricing Available For The First 50 Customers Only! (ORDER XR Massive Male Enhancement)
[STEPS] | [] |
96,460 | Cell Lysate Preparation & Immunoblotting Protocols | 0 | dx.doi.org/10.17504/protocols.io.yxmvm3dwnl3p/v1 | https://www.protocols.io/view/cell-lysate-preparation-amp-immunoblotting-protoco-dafk2bkw | Caitlyn Henry | TITLE: Cell Lysate Preparation & Immunoblotting Protocols
AUTHORS: Caitlyn Henry
[DESCRIPTION]
The purpose of this experiment is to investigate the effects of forskolin-mediated cAMP activation on NF-κB, TNF-ɑ, AKAP95, and cyclin D3 expression in LPS-treated Schwann cells. The immortalized rat RT4-D6P2T cell line ... | ["[To prepare RT4-D6P2T cell lysates (for three 6-well plates):] Aseptically culture immortalized rat RT4-D6P2T Schwann cells (ATCC, Cat #CRL-2768, Manassas, VA) in Dulbecco’s Modified Eagle Medium (DMEM) (ATCC, Cat #30-2002, Manassas, VA) supplemented with 10% fetal bovine serum (FBS) (Thermo Fisher, Cat #16000044, Wa... |
46,201 | VU Biomolecular Multimodal Imaging Center (BIOMIC) Eye characterization pipeline | 1 | dx.doi.org/10.17504/protocols.io.j8nlk49w5g5r/v1 | https://www.protocols.io/view/vu-biomolecular-multimodal-imaging-center-biomic-e-brczm2x6 | Angela R.S. Kruse, David Anderson, Jeffrey D. Messinger, Jamie Allen, Lukasz Migas, ali.zahraei, ellie.l.pingry, Morad C Malek, Audramjudd, Dongfeng Cao, Melissa Farrow, Christine A. Curcio, Raf Van De Plas, Kevin Schey, Jeff Spraggins | TITLE: VU Biomolecular Multimodal Imaging Center (BIOMIC) Eye characterization pipeline
AUTHORS: Angela R.S. Kruse, David Anderson, Jeffrey D. Messinger, Jamie Allen, Lukasz Migas, ali.zahraei, ellie.l.pingry, Morad C Malek, Audramjudd, Dongfeng Cao, Melissa Farrow, Christine A. Curcio, Raf Van De Plas, Kevin Schey, J... | ["[Organ Procurement and Processing] Collaborating with the Advancing Sight Network (500 Robert Jemison Rd Birmingham, AL 35209), our team identifies and preserves human donor ocular tissue using the following protocols. \n\nDonor Tissue Acceptance Criteria:\n1. Caucasian or African American (AA)\n2. ≥18-70 years of ag... |
101,277 | Protocol for the growth and maintenance of mammalian cell lines | 0 | dx.doi.org/10.17504/protocols.io.8epv5rrq4g1b/v1 | https://www.protocols.io/view/protocol-for-the-growth-and-maintenance-of-mammali-de553g86 | Agnes Roczniak-Ferguson, Shawn M. Ferguson | TITLE: Protocol for the growth and maintenance of mammalian cell lines
AUTHORS: Agnes Roczniak-Ferguson, Shawn M. Ferguson
[DESCRIPTION]
This protocol details about the growth and maintenance of mammalian cell lines.
[STEPS]
SECTION: The following protocol was written for HeLa cells but can be adapted to many other s... | ["[The following protocol was written for HeLa cells but can be adapted to many other standard mammalian cell lines.] Remove 1x PBS, trypsin, and media (DMEM+10%FBS+1%pen/strep supplement (Gibco) from the fridge and warm it up in a 37 °C water bath for 10 min.", "[The following protocol was written for HeLa cells but c... |
46,105 | Anxiety of pregnant women in time of catastrophic events, including COVID-19 pandemic – a systematic review and metanalysis protocol. | 1 | dx.doi.org/10.17504/protocols.io.bq9zmz76 | https://www.protocols.io/view/anxiety-of-pregnant-women-in-time-of-catastrophic-bq9zmz76 | Stepan Feduniw, Jan Modzelewski, Dorota Sys, Sebastian Kwiatkowski, Anna Kajdy | TITLE: Anxiety of pregnant women in time of catastrophic events, including COVID-19 pandemic – a systematic review and metanalysis protocol.
AUTHORS: Stepan Feduniw, Jan Modzelewski, Dorota Sys, Sebastian Kwiatkowski, Anna Kajdy
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "jus... | ["[INTRODUCTION]\nThe perinatal period is often a time of maternal emotional distress related to the pregnancy itself. Women are concerned with fetal wellbeing and labor outcome. Besides the pregnancy itself, there are several risk factors correlated with a higher prevalence of anxiety1. Risk factors of anxiety include... |
106,611 | Induced Cortical Neuron Differentiation - Part 2 - Day 0 Dissociation | 0 | dx.doi.org/10.17504/protocols.io.n92ld81y9v5b/v1 | https://www.protocols.io/view/induced-cortical-neuron-differentiation-part-2-day-dkct4swn | Isabel Lam, Alain Ndayisaba, Vikram Khurana | TITLE: Induced Cortical Neuron Differentiation - Part 2 - Day 0 Dissociation
AUTHORS: Isabel Lam, Alain Ndayisaba, Vikram Khurana
[DESCRIPTION]
Induced Cortical Neuron Differentiation - Part 2 - Day 0 Dissociation
[STEPS] | [] |
59,822 | Total RNA and DNA from Microalgae (24 samples per day) | 1 | null | https://www.protocols.io/view/total-rna-and-dna-from-microalgae-24-samples-per-d-b6nnrdde | Yingyu Hu, Zoe V Finkel | TITLE: Total RNA and DNA from Microalgae (24 samples per day)
AUTHORS: Yingyu Hu, Zoe V Finkel
[DESCRIPTION]
Here we describe a protocol for extracting and quantifying bulk RNA and DNA from microalgae, which is adapted from Berdalet E. et al. (2005).
RNA and DNA are extracted from microalgae samples and then quant... | ["[Day 1: Freeze-dry samples] Freeze dry samples and blank filters. Freeze at -80 °C until processed.", "[Day 1: Prepare primary solutions] Turn on UV light in biosafety cabinet for 15 min and clean working surface with decontamination solution.", "[Day 1: Prepare primary solutions] Prepare Tris buffer 5 mM pH 8.0", ... |
null | null | null | dx.doi.org/10.17504/protocols.io.hd7b29n | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?. | [] |
69,884 | Intracellular neuromelanin quantification | 4 | dx.doi.org/10.17504/protocols.io.yxmvm27e6g3p/v1 | https://www.protocols.io/view/intracellular-neuromelanin-quantification-cgg4ttyw | miquel.vila | TITLE: Intracellular neuromelanin quantification
AUTHORS: miquel.vila
[DESCRIPTION]
Protocol for quantifying intracellular neuromelanin
[STEPS]
1. Scan midbrain section using the Pannoramic Midi II FL, HQ Scientific 60x
2. Acquire SNpc images at 63x with CaseViewer
3. Upload individual images at Image J software
4. ... | ["Scan midbrain section using the Pannoramic Midi II FL, HQ Scientific 60x", "Acquire SNpc images at 63x with CaseViewer", "Upload individual images at Image J software", "Click on Adjust canvas size and adjust it at 1596x1198", "Click on Invert image", "With the free hand selections tool, draft a neuromelanin-pigmente... |
52,489 | FindingNemo Library 1: Modified ULK001 | 1 | dx.doi.org/10.17504/protocols.io.bxhhpj36 | https://www.protocols.io/view/findingnemo-library-1-modified-ulk001-bxhhpj36 | Inswasti Cahyani, John Tyson, Nadine Holmes, Josh Quick, Nicholas Loman, Matthew Loose | TITLE: FindingNemo Library 1: Modified ULK001
AUTHORS: Inswasti Cahyani, John Tyson, Nadine Holmes, Josh Quick, Nicholas Loman, Matthew Loose
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This sub-protocol is designed to prepare library from extracted ultra-high molecular weight (UHMW) DNA t... | ["[Transposase Reaction]\nIn a 2 ml tube, dilute UHMW DNA to a concentration of around 50 ng/μl in a total volume of 750 μl (with water or elution buffer if required).Mix well with a P1000 wide-bore tip. Cell No. (million)Approx. DNA amount (μg)Total DNA volume (μl)DNA concentration (ng/μl)Total reaction volume (μl)6>2... |
61,698 | Optimizing the electroporation parameters for Heterometopus palaeformis (strain RAJCA) | 4 | dx.doi.org/10.17504/protocols.io.rm7vzy78rlx1/v1 | https://www.protocols.io/view/optimizing-the-electroporation-parameters-for-hete-b8hart2e | Fatma Gomaa, Johana Rotterova, Roxanne Beinart, Maria Pachiadaki, Virginia Edgcomb | TITLE: Optimizing the electroporation parameters for Heterometopus palaeformis (strain RAJCA)
AUTHORS: Fatma Gomaa, Johana Rotterova, Roxanne Beinart, Maria Pachiadaki, Virginia Edgcomb
[DESCRIPTION]
Cell viability after incubation with different electroporation buffers,
Phosphate buffered saline (PBS) is used a... | [] |
47,271 | LAMP/RT-LAMP Reaction protocol | 1 | dx.doi.org/10.17504/protocols.io.bsefnbbn | https://www.protocols.io/view/lamp-rt-lamp-reaction-protocol-bsefnbbn | Tamara Matute, Isaac Núñez, Fernan Federici | TITLE: LAMP/RT-LAMP Reaction protocol
AUTHORS: Tamara Matute, Isaac Núñez, Fernan Federici
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes how to perform </span><span style = "font-weight:bold;">LAMP / RT-LAMP reactions with home-made reagents</span><span>, which means ... | ["[Primers Stock]\nPrepare 10X LAMP Primer Mix stock according to the following table:", "[Primers Stock]\nPrepare stocks (100μM) of each primer in nuclease-free water and store at –20°C for up to 2 years.", "[Reaction]\nVortex and spin reaction mix.\non ice\nIf you need to add different samples; pipet per reaction i... |
36,943 | Phenotyping 3D coral models in MeshLab | 1 | dx.doi.org/10.17504/protocols.io.bgbpjsmn | https://www.protocols.io/view/phenotyping-3d-coral-models-in-meshlab-bgbpjsmn | Wyatt Million, Carly Kenkel | TITLE: Phenotyping 3D coral models in MeshLab
AUTHORS: Wyatt Million, Carly Kenkel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes the process of phenotyping branching coral using the 3D model editing software, MeshLab. MeshLab is a free, straightforward software to ana... | ["Open your 3D model file in MeshLab. Wavefront (.obj) is one 3D file format that can be exported by Metashape. We recommend using this format because .obj files can be exported with color included. Having color in the models is especially important when cropping the model down to just the coral. You can test out this ... |
49,591 | Collecting samples for Dissolved Organic Carbon (DOC) analysis | 1 | null | https://www.protocols.io/view/collecting-samples-for-dissolved-organic-carbon-do-bunxnvfn | Krista Longnecker | TITLE: Collecting samples for Dissolved Organic Carbon (DOC) analysis
AUTHORS: Krista Longnecker
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes collecting samples for Dissolved Organic Carbon (DOC) analysis. Dissolved organic carbon is operationally defined as the material t... | ["[Collecting samples for Total Organic Carbon (TOC) analysis]\nThe glass vials need to be combusted before use.", "[Collecting samples for Total Organic Carbon (TOC) analysis]\nSet aside the caps that were sent with the vials because they cannot be combusted.", "[Collecting samples for Total Organic Carbon (TOC) analy... |
46,972 | Pseudotyping lentiviral particles with SARS-CoV-2 Spike protein for neutralization assays | 1 | dx.doi.org/10.17504/protocols.io.br44m8yw | https://www.protocols.io/view/pseudotyping-lentiviral-particles-with-sars-cov-2-br44m8yw | Katharine H. D. Crawford, Rachel Eguia, Adam S. Dingens, Andrea N. Loes, Jesse D. Bloom | TITLE: Pseudotyping lentiviral particles with SARS-CoV-2 Spike protein for neutralization assays
AUTHORS: Katharine H. D. Crawford, Rachel Eguia, Adam S. Dingens, Andrea N. Loes, Jesse D. Bloom
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">SARS-CoV-2 enters cells using its Spike protein, which is ... | ["[Generation of Pseudotyped Lentiviral Particles]\nSeed 293T cell in D10 Growth Media so they will be 50-70% confluent the next day.\nFor a 6-well plate, this is 5x105 cells per well (2.5x105 cells per mL).", "[Generation of Pseudotyped Lentiviral Particles]\nAt 16-24 hours after seeding, transfect the cells with the ... |
88,605 | The relationship and interaction between stress-induced inflammation and the gut-brain (GBA) axis in the future development of post-traumatic stress disorder (PTSD) or post-traumatic stress symptoms: a systematic review | 3 | dx.doi.org/10.17504/protocols.io.8epv5xnq4g1b/v1 | https://www.protocols.io/view/the-relationship-and-interaction-between-stress-in-c2r5yd86 | jyoo, Kayla Kucela, speret, Allie Cooper, Samia Valeria Ozorio Dutra | TITLE: The relationship and interaction between stress-induced inflammation and the gut-brain (GBA) axis in the future development of post-traumatic stress disorder (PTSD) or post-traumatic stress symptoms: a systematic review
AUTHORS: jyoo, Kayla Kucela, speret, Allie Cooper, Samia Valeria Ozorio Dutra
[DESCRIPTION]
... | [] |
23,888 | Neuropathy Phentoyping Protocols - Dosages of Tranquilizers and Anesthetics for Mice, Rats, Hamsters/Gerbils | null | dx.doi.org/10.17504/protocols.io.3jqgkmw | null | Eva Feldman | TITLE: Neuropathy Phentoyping Protocols - Dosages of Tranquilizers and Anesthetics for Mice, Rats, Hamsters/Gerbils
AUTHORS: Eva Feldman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block"><span style = "font-weight:bold;">... | [] |
40,706 | Improved protocol of ELISA for determining the serum concentration of IL-23 in humans. | 4 | dx.doi.org/10.17504/protocols.io.bjzakp2e | https://www.protocols.io/view/improved-protocol-of-elisa-for-determining-the-ser-bjzakp2e | Angel Justiz-Vaillant | TITLE: Improved protocol of ELISA for determining the serum concentration of IL-23 in humans.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">A previous protocol was contaminated with IL-17. This is an improved version of an ELISA for quantification of Interleukin 23.... | ["Ninety-six well ELISA plates are coated with monoclonal anti-human antibodies to interleukin-23 (IL-23).", "Patient serum samples are added to the plates.", "The plate is incubate x 1.30 hour at RT.", "The plate is washed 4 times with PBS-tween 20 buffer.", "The wells are incubated with a biotin conjugated anti-human... |
78,538 | 3. Codes for bioinformatics and statistical data analysis | 1 | dx.doi.org/10.17504/protocols.io.e6nvwj4bzlmk/v1 | https://www.protocols.io/view/3-codes-for-bioinformatics-and-statistical-data-an-cqxivxke | Haydeh Payami | TITLE: 3. Codes for bioinformatics and statistical data analysis
AUTHORS: Haydeh Payami
[DESCRIPTION]
This protocol details the codes for bioinformatics and statistical data analysis.
[STEPS]
SECTION: Codes for bioinformatics and statistical data analysis
1.
SECTION: Codes for bioinformatics and statistical data ... | ["[Codes for bioinformatics and statistical data analysis]", "[Codes for bioinformatics and statistical data analysis]"] |
null | null | null | dx.doi.org/10.17504/protocols.io.espbedn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in <a href="https://www.protocols.io/view/CviJI-Purification-From-IL-3A-Virus-Infected-NC64A-er3bd8n" target="_blank">CviJI Purification From IL-3A Virus Infected NC64A Chlorella</a>.
[STEPS]
?.
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80,826 | Community-based cross-sectional survey | 1 | dx.doi.org/10.17504/protocols.io.rm7vzbpjrvx1/v1 | https://www.protocols.io/view/community-based-cross-sectional-survey-cs62whge | Kajiru Gad Kilonzo, Stefanie J. Krauth, Jo Halliday, Clive Kelly, Stefan Siebert, Gloria Temu, Christopher Bunn, Nateiya M Yongolo, Sally Wyke, Emma McIntosh, Blandina Mmbaga | TITLE: Community-based cross-sectional survey
AUTHORS: Kajiru Gad Kilonzo, Stefanie J. Krauth, Jo Halliday, Clive Kelly, Stefan Siebert, Gloria Temu, Christopher Bunn, Nateiya M Yongolo, Sally Wyke, Emma McIntosh, Blandina Mmbaga
[DESCRIPTION]
This protocol details community-based cross-sectional survey.
[GUIDELINES]... | ["[Participant selection] Based on sample-size calculations, the study will recruit 1050 households (approximately 5701 individuals) for this cross-sectional survey, to achieve a confidence level of 95% and assuming a 15% prevalence of MSK (as estimated in the pilot study).", "[Participant selection] Two-stage cluster ... |
66,372 | Condor CBD Gummies Shark Tank Reviews (Where to Buy?) Real Customer Exposed & Worth Of Money! | 3 | dx.doi.org/10.17504/protocols.io.bp2l6169rvqe/v1 | https://www.protocols.io/view/condor-cbd-gummies-shark-tank-reviews-where-to-buy-cc3csyiw | Condor CBD Gummies Price | TITLE: Condor CBD Gummies Shark Tank Reviews (Where to Buy?) Real Customer Exposed & Worth Of Money!
AUTHORS: Condor CBD Gummies Price
[DESCRIPTION]
Health
[STEPS] | [] |
26,304 | ASSESSING RTTA ACTIVITY (Support Protocol 6) | null | dx.doi.org/10.17504/protocols.io.5w8g7hw | null | Michael S. Fernandopulle, Ryan Prestil, Christopher Grunseich, Chao Wang, Li Gan, Michael E. Ward | TITLE: ASSESSING RTTA ACTIVITY (Support Protocol 6)
AUTHORS: Michael S. Fernandopulle, Ryan Prestil, Christopher Grunseich, Chao Wang, Li Gan, Michael E. Ward
[STEPS]
?. Prepare four wells of the cell line of interest by EDTA split (Basic Protocol 1).
For at least the first time performing this protocol, include posi... | ["Prepare four wells of the cell line of interest by EDTA split (Basic Protocol 1).\nFor at least the first time performing this protocol, include positive and negative control cells in order to compare with cells of interest.", "1 to 2 days after plating, follow Basic Protocol 2 (steps 6 to 9) for two of the wells in ... |
102,450 | GenFS Metadata Cleanup Challenge protocol | 0 | dx.doi.org/10.17504/protocols.io.rm7vzj6prlx1/v1 | https://www.protocols.io/view/genfs-metadata-cleanup-challenge-protocol-dgas3see | Ruth Timme, Martin Shumway, Candace Hope Bias, Maria Balkey, Tina Lusk Pfefer | TITLE: GenFS Metadata Cleanup Challenge protocol
AUTHORS: Ruth Timme, Martin Shumway, Candace Hope Bias, Maria Balkey, Tina Lusk Pfefer
[DESCRIPTION]
This protocol provides guidance for submitting bulk BioSample updates to NCBI for the GenFS Metadata Cleanup Challenge exercise.
Table of Contents:
Timeline/Workflow f... | ["[Guidance for preparing the update file] Prepare the update file:\n\nUpdates should be put into one bulk update file per lab, or per lab/organism, or some other aggregation. \nRows: The first row, or header, must contain the column names. Each subsequent row must contain exactly one BioSample and its updatable field... |
92,551 | Modular automated sample processing of biological samples using ultrasonication and a workstation for high-throughput proteomics | 2 | dx.doi.org/10.17504/protocols.io.j8nlkoy56v5r/v2 | https://www.protocols.io/view/modular-automated-sample-processing-of-biological-c6mfzc3n | ronan.ocualain | TITLE: Modular automated sample processing of biological samples using ultrasonication and a workstation for high-throughput proteomics
AUTHORS: ronan.ocualain
[DESCRIPTION]
Sample preparation for mass spectrometry analysis involves numerous liquid transfer steps.
These include
sample lysis,
protein extraction,
so... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.h82b9ye | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
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57,237 | Embryo stage C. elegans dissociation for FACS isolation and RNA-seq analysis of intestine-specific cells | 4 | dx.doi.org/10.17504/protocols.io.dm6gpbw9plzp/v1 | https://www.protocols.io/view/embryo-stage-c-elegans-dissociation-for-facs-isola-b35vqq66 | Robert TP Williams, Erin Osborne Nishimura | TITLE: Embryo stage C. elegans dissociation for FACS isolation and RNA-seq analysis of intestine-specific cells
AUTHORS: Robert TP Williams, Erin Osborne Nishimura
[DESCRIPTION]
This protocol is for generating a single cell suspension suitable for isolation of intestine-specific cells through Fluorescence Activated C... | ["[Chitinase Treatment] Centrifuge embryo suspension at 2000 rcf for 1 minute in swinging bucket centrifuge", "[Chitinase Treatment] Transfer 10 ul of embryo pellet to 1ml of Qiazol and store at -80°C for downstream RNA analysis", "[Chitinase Treatment] Resuspend the embryo pellet from Step 7 in 0.5 ml egg buffer and 1... |
44,896 | A Brief Look of Univariate Analysis | 4 | null | https://www.protocols.io/view/a-brief-look-of-univariate-analysis-bp38mqrw | 181830691 , FDF | TITLE: A Brief Look of Univariate Analysis
AUTHORS: 181830691 , FDF
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Univariate analysis mainly focuses on the description of univariate and statistical inference. It uses the simplest general form to reflect the basic information contained in a large n... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.rvvd666 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Preparation of giant unilamellar vesicels (GUVs) by electroformation method has been detailed. 10 to 100 micrometer size GUVs obtained after the process. </p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
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?.
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?. | [] |
52,275 | High-quality reference genome of Fasciola gigantica: Insights into the genomic signatures of transposon-mediated evolution and specific parasitic adaption in tropical regions | 4 | dx.doi.org/10.17504/protocols.io.bxatpien | https://www.protocols.io/view/high-quality-reference-genome-of-fasciola-gigantic-bxatpien | Xier Luo | TITLE: High-quality reference genome of Fasciola gigantica: Insights into the genomic signatures of transposon-mediated evolution and specific parasitic adaption in tropical regions
AUTHORS: Xier Luo
[DESCRIPTION]
Fasciola gigantica and Fasciola hepatica are causative pathogens of fascioliasis, with the widest latitu... | ["Sample collection\nAll animal work was approved by the Guangxi University Institutional Animal Care and Use Committee. For the reference genome sequencing, one F. gigantica at adult stage was derived from infected buffalo in the Guangxi Zhuang Autonomous Region.", "De novo sequencing and assembly", "Genome annotation... |
null | null | null | dx.doi.org/10.17504/protocols.io.ecubaww | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
45,154 | Validation of Genotyping Method for L444P Mice Ear-Clips | 4 | dx.doi.org/10.17504/protocols.io.261ge4dewv47/v1 | https://www.protocols.io/view/validation-of-genotyping-method-for-l444p-mice-ear-bqcamsse | Revi Shahar Golan, David C | TITLE: Validation of Genotyping Method for L444P Mice Ear-Clips
AUTHORS: Revi Shahar Golan, David C
[DESCRIPTION]
Aim: the genotyping is used to identify if mice are heterozygote (hetero) or Wild-Type (WT), and the aim of the work is to validate the digestion method, and PCR program, the PCR primers, and the interpret... | ["[Digestion] Prepare Digestion mix: 15 µL (Roche, cat 10241100) per 1000 µL (Viagen, cat 402-E).", "[Digestion] Add 50 µL to each ear clip sample.", "[PCR] Prepare PCR master mix (MM) as below (per sample):\n\n2.5 µL (VWR-Peqlab, cat 01-1020) \n0.25 µL (VWR-Peqlab, cat 01-1020) \n0.5 µL (10pmol/ µl)\n0.5 µL (10pmol/ µ... |
38,895 | Taxonomic classification of IonTorrent-sequenced 16S amplicon sequences | 5 | dx.doi.org/10.17504/protocols.io.bh8pj9vn | https://www.protocols.io/view/taxonomic-classification-of-iontorrent-sequenced-1-bh8pj9vn | Laura Espina | TITLE: Taxonomic classification of IonTorrent-sequenced 16S amplicon sequences
AUTHORS: Laura Espina
[STEPS]
?. [Pre-processing]
Demultiplex sequences. Quality-filter sequences. Tim barcodes and adapters. Export as fastq files (1 fastq file per sample).
Example of fastq files at this point:
?. [Pre-processing]
Import ... | ["[Pre-processing]\nDemultiplex sequences. Quality-filter sequences. Tim barcodes and adapters. Export as fastq files (1 fastq file per sample).\nExample of fastq files at this point:", "[Pre-processing]\nImport fastq files.Trim primers.Remove sequences shorter than 100 bp.Suggested software:(or python scripts).", "[Pr... |
64,384 | 7 Day Challenge Wonder Leaf CBD Oil Diet + Improve Metabolism | 3 | dx.doi.org/10.17504/protocols.io.yxmvmnmjbg3p/v1 | https://www.protocols.io/view/7-day-challenge-wonder-leaf-cbd-oil-diet-improve-m-ca48sgzw | Wonder Leaf CBD Oil | TITLE: 7 Day Challenge Wonder Leaf CBD Oil Diet + Improve Metabolism
AUTHORS: Wonder Leaf CBD Oil
[DESCRIPTION]
►Wonder Leaf CBD Oil – Official Website Link – Click Here
[STEPS] | [] |
54,970 | Chlamydia pneumoniae-Induced Neuroinflammation Cell Model Using Lyophilized Cell-Free Supernatant | 4 | dx.doi.org/10.17504/protocols.io.bzw2p7ge | https://www.protocols.io/view/chlamydia-pneumoniae-induced-neuroinflammation-cel-bzw2p7ge | Elif Kaya Tilki | TITLE: Chlamydia pneumoniae-Induced Neuroinflammation Cell Model Using Lyophilized Cell-Free Supernatant
AUTHORS: Elif Kaya Tilki
[DESCRIPTION]
Chlamydia pneumoniae (Cpn) is a gram-negative intracellular pathogen that causes a variety of pulmonary diseases, and there is growing evidence that it may play a role in A... | ["HEp-2 cells were used as a host to inoculate Chlamydia pneumoniae. A 6-well plate of 1X106 HEp-2 cells was seeded 48 hours prior to inoculation with Chlamydia pneumoniae (ATCC 53592).", "The suspension of elementary bodies diluted in infection medium was added directly to wells.", "The mixture was centrifuged at 1500... |
62,759 | Fixation of yeast cells for RNA-FISH | 1 | null | https://www.protocols.io/view/fixation-of-yeast-cells-for-rna-fish-b9ifr4bn | Lenny Teytelman, Arjun Raj | TITLE: Fixation of yeast cells for RNA-FISH
AUTHORS: Lenny Teytelman, Arjun Raj
[DESCRIPTION]
This protocol is for S. cerevisiae and is a modification of the one developed and used by Arjun Raj and his colleagues for:
Raj A, van den Bogaard P, Rifkin SA, van Oudenaarden A, Tyagi S. Imaging individual mRNA molecules... | ["[Inoculation and Growth] Around 10am, start a cell culture in a 50ml tube, using 10ml of CSM.", "[Inoculation and Growth] Grow for 8-10 hours in a shaker at 30 °C.\n480 min", "[Inoculation and Growth] Measure OD in the evening and dilute into 250ml glass flasks, starting 45ml of CSM for overnight growth. Aiming for O... |
48,565 | Extraction of DNA from endocervical samples using QIAamp DNA mini kit | 3 | dx.doi.org/10.17504/protocols.io.btnvnme6 | https://www.protocols.io/view/extraction-of-dna-from-endocervical-samples-using-btnvnme6 | emmanuelgomseu EBDG EBDG Boris Emmanuel DJOUMSIE GOMSEU | TITLE: Extraction of DNA from endocervical samples using QIAamp DNA mini kit
AUTHORS: emmanuelgomseu EBDG EBDG Boris Emmanuel DJOUMSIE GOMSEU
[DESCRIPTION]
DNA was extracted from endocervical samples using the QIAamp mini kit according to the manufacturer’s instructions.
1 Centrifuge tubes containing the endocervical... | [] |
91,566 | Spot detection on structured background protocol | 5 | dx.doi.org/10.17504/protocols.io.36wgq3y23lk5/v1 | https://www.protocols.io/view/spot-detection-on-structured-background-protocol-c5nny5de | Bin Fu | TITLE: Spot detection on structured background protocol
AUTHORS: Bin Fu
[DESCRIPTION]
This protocol details the steps for using the spot detection code
[STEPS]
1. Put sub-diffraction beads images in the folder ‘area_threshold’ and run determineAreaThres.m to find the maximum area in pixel for a diffraction-limited ob... | ["Put sub-diffraction beads images in the folder ‘area_threshold’ and run determineAreaThres.m to find the maximum area in pixel for a diffraction-limited object.", "Put negative control images in the folder ‘negative_control’ and run determineRad.m to determined the steepness and integrated gradient used in the study.... |
54,428 | LCMSMethods.org 2019 release | 2 | dx.doi.org/10.17504/protocols.io.bzd4p28w | https://www.protocols.io/view/lcmsmethods-org-2019-release-bzd4p28w | Benjamin Orsburn | TITLE: LCMSMethods.org 2019 release
AUTHORS: Benjamin Orsburn
[DESCRIPTION]
This is the original batch of instrument methods collected for the LCMSMethods.org release at ASMS 2019. This batch of methods was created by Ben Orsburn to get the site rolling and only contains methods for Thermo Fisher Scientific Mass Spect... | [] |
88,925 | Yale Murine TMC - Frozen Tissue Sectioning Protocol for Spatial Transcriptomics (DBiTSeq) and Immunofluorescence | 1 | dx.doi.org/10.17504/protocols.io.j8nlko3dwv5r/v1 | https://www.protocols.io/view/yale-murine-tmc-frozen-tissue-sectioning-protocol-c235ygq6 | Yun-Hee Youm, Yufeng Liu, Bo Tao, Vishwa Deep Dixit, Rong Fan | TITLE: Yale Murine TMC - Frozen Tissue Sectioning Protocol for Spatial Transcriptomics (DBiTSeq) and Immunofluorescence
AUTHORS: Yun-Hee Youm, Yufeng Liu, Bo Tao, Vishwa Deep Dixit, Rong Fan
[DESCRIPTION]
Protocol for frozen tissue sectioning for use in DBiTSeq and immunofluorescence staining
[STEPS]
SECTION: Tiss... | ["[Tissue Embedding] Embed tissue according to this protocol: dx.doi.org/10.17504/protocols.io.kqdg3x8keg25/v1", "[Cryosectioning] Spray the workplace and tools (blades, tweezers, brushes, etc) with RNAseZap to decontaminate the environment. Spray 100% ethanol onto the cryostat to remove any residue of RNAseZap or rea... |
26,691 | Genomic DNA extraction from animal faecal tissues using DNeasy blood and tissue kit | null | dx.doi.org/10.17504/protocols.io.6bbhain | null | Somasundhari Shanmuganandam, Benjamin Schwessinger, Robyn Hall | TITLE: Genomic DNA extraction from animal faecal tissues using DNeasy blood and tissue kit
AUTHORS: Somasundhari Shanmuganandam, Benjamin Schwessinger, Robyn Hall
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Faecal tissues are difficult to lyse and contain lower amount of DNA compared to other an... | ["[Tissue subculturing]\nThaw the samples in ice and bring it to room temperature", "Using a scapel, place the tissue in a petri dish and cut 50 mg of tissue. Check the tissue weight to confirm. Place it in a 2 ml eppendorf tube filled with 0.5 cm of purified silica beads.", "[DNA extraction]\nAdd 324 μl of buffer ATL ... |
77,305 | Identification of a Plasmid: Transformation | 4 | dx.doi.org/10.17504/protocols.io.8epv5jmj6l1b/v1 | https://www.protocols.io/view/identification-of-a-plasmid-transformation-cpqzvmx6 | SGD | TITLE: Identification of a Plasmid: Transformation
AUTHORS: SGD
[DESCRIPTION]
Protocol for the identification of a plasmid by using transformation of E. Coli
[STEPS]
SECTION: Transformation
1. Transfer 1 mL E. Coli to each of two 1.5 mL Eppendorf tube
SECTION: Transformation
2. Centrifuge at full speed for 30 s, the... | ["[Transformation] Transfer 1 mL E. Coli to each of two 1.5 mL Eppendorf tube", "[Transformation] Centrifuge at full speed for 30 s, then remove the supernatant", "[Transformation] Add 450 µL of TFB1 to each tube, then resuspend gently by pipetting up and down (do not vortex)\nKeep everything on ice\nIncubate on ice fo... |
28,282 | Supporting information 1 (Yuzhalin et al. 2019) | null | dx.doi.org/10.17504/protocols.io.7u2hnye | null | Yuzhalin AE, Lim SY, Gordon-Weeks AN, Roman Fischer, Kessler BM, Dihua Yu, Muschel RJ | TITLE: Supporting information 1 (Yuzhalin et al. 2019)
AUTHORS: Yuzhalin AE, Lim SY, Gordon-Weeks AN, Roman Fischer, Kessler BM, Dihua Yu, Muschel RJ
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Supporting Information 1. Raw results obtained from quantitative label-free proteomics analysis of dec... | [] |
53,136 | 3D Reconstruction of Neurons in Vaa3D v 3 | 1 | null | https://www.protocols.io/view/3d-reconstruction-of-neurons-in-vaa3d-v-3-bx5qpq5w | Allen Institute for Brain Science | TITLE: 3D Reconstruction of Neurons in Vaa3D v 3
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used to generate accurate digital representations of neuron morphologies from a variety of brain regions and species. Each reconstruction captu... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.hhxb37n | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?. | [] |
95,779 | Recombinant αS purification Protocol | 1 | dx.doi.org/10.17504/protocols.io.q26g7popkgwz/v1 | https://www.protocols.io/view/recombinant-s-purification-protocol-c9sbz6an | Jane Balster | TITLE: Recombinant αS purification Protocol
AUTHORS: Jane Balster
[DESCRIPTION]
This protocol details the recombinant αS purification.
[STEPS]
SECTION: Culture Growth and Induction
1. Day 1: Inoculate 5 mL of LB/Amp [100 1527: 1 µL of 100 1524 Amp stock (freezer) for every 1 mL of culture] with 1 colony from LB/Amp p... | ["[Culture Growth and Induction] Day 1: Inoculate 5 mL of LB/Amp [100 1527: 1 µL of 100 1524 Amp stock (freezer) for every 1 mL of culture] with 1 colony from LB/Amp plate and put in a shaker at 37 °C w/ .\n\nModification:\n\nInoculate 10 mL of LB/Amp with 1 colony (allows more rapid growth).\n\nIf no viable plate:\n... |
51,484 | Smart-seq3xpress | 1 | dx.doi.org/10.17504/protocols.io.yxmvmk1yng3p/v1 | https://www.protocols.io/view/smart-seq3xpress-bwh4pb8w | Michael Hagemann-Jensen, Christoph Ziegenhain, Rickard Sandberg | TITLE: Smart-seq3xpress
AUTHORS: Michael Hagemann-Jensen, Christoph Ziegenhain, Rickard Sandberg
[DESCRIPTION]
Plate-based single-cell RNA-sequencing methods with full-transcript coverage typically excel at sensitivity but are more resource and time-consuming. Here, we miniaturized and streamlined the Smart-seq3 pro... | ["[Before Starting] This protocol should be carried out in a clean environment. Use ethanol, RNAseZAP, DNA-OFF, or similar to prepare work bench before start.\n\nWork quickly and preferably on ice.\n\nTry and prepare master-mixes right before use, while the plate(s) are finishing the previous incubation step.", "[Prepa... |
null | null | null | dx.doi.org/10.17504/protocols.io.dx37qm | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
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22,458 | UV Crosslinking of Suspension Cells for eCLIP | null | dx.doi.org/10.17504/protocols.io.z62f9ge | null | Eric Van Nostrand, Gene Yeo | TITLE: UV Crosslinking of Suspension Cells for eCLIP
AUTHORS: Eric Van Nostrand, Gene Yeo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Profiling of RNA binding protein targets in vivo provides critical insights into the mechanistic roles they play in regulating RNA processing. The enhanced crossl... | ["[UV Crosslinking]\nAliquot at most 60×106 cells (re-suspended in 1x DPBS) in at least 3 mL total volume to a standard 10cm tissue culture grade plate.", "[UV Crosslinking]\nPlace the above (plate plus ice or cooling block) into the UV cross-linker. Note: Ensure the plate is leveled. Remove tissue culture plate lid ... |
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