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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null | null | null | dx.doi.org/10.17504/protocols.io.ddd225 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This medium is used successfully for most cyanobacteria. Vitamin B<sub>12</sub> may be added for those species that require it. Use f/2 vitamin solution.
[GUIDELINES]
<table>
<tbody>
<tr>
<td><strong>STOCK</strong></td>
<td><strong>STOCK SOLUTION</strong></td>
<td><strong... | [] |
52,597 | Microfluidics 6: PDMS Chip, Optical Quality Control and Flow Leakage Test | 1 | dx.doi.org/10.17504/protocols.io.bxkvpkw6 | https://www.protocols.io/view/microfluidics-6-pdms-chip-optical-quality-control-bxkvpkw6 | Serhat Sevli, C. Yunus Sahan | TITLE: Microfluidics 6: PDMS Chip, Optical Quality Control and Flow Leakage Test
AUTHORS: Serhat Sevli, C. Yunus Sahan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">Fabrication of microfluidic chips requires high quality and high resolution manufac... | ["[Chip Quality Control]\nOptical Quality Control of the microfluidic chips are performed by using digital microscope. The visual parameters checked for acceptance of the chip are as listed below. Defects and scratchsStrains and voidsDirt in featuresAir bubbles in featuresPorts and Bonding, out of alignmentNot bond fea... |
51,468 | Data update | 5 | dx.doi.org/10.17504/protocols.io.bwhkpb4w | https://www.protocols.io/view/data-update-bwhkpb4w | Alise J. Ponsero | TITLE: Data update
AUTHORS: Alise J. Ponsero
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocols aims to details the steps necessary to update previously collected data points for the "Database Justice League" project.</div></div>
[STEPS]
?. [Download data]
Once you have received the lin... | ["[Download data]\nOnce you have received the link to download your dataset, download the csv file locally.Make sure to save it on your computer in a convenient folder!In this protocol we will perform the data collection on a test dataset:", "[Download data]\nAs you can see in this test dataset, some preliminary inform... |
86,423 | Open Science for Social Sciences and Humanities: Open Access availability and distribution across disciplines and Countries in OpenCitations Meta - PROTOCOL | 5 | dx.doi.org/10.17504/protocols.io.5jyl8jo1rg2w/v5 | https://www.protocols.io/view/open-science-for-social-sciences-and-humanities-op-cymxxu7n | Ali Ghasempouri, maddalena.ghiotto, sebastiano.giacomini | TITLE: Open Science for Social Sciences and Humanities: Open Access availability and distribution across disciplines and Countries in OpenCitations Meta - PROTOCOL
AUTHORS: Ali Ghasempouri, maddalena.ghiotto, sebastiano.giacomini
[DESCRIPTION]
In this study, we present the workflow followed for the research workflow t... | ["[Data Used] ERIH PLUS index of Social Sciences and Humanities approved journals dataset (2MB, downloaded 27/04/2023)\n \n\nOpenCitations Meta data dump (36 MB, downloaded in the version of 24/02/2023)\n\n \n\nDOAJ, the Directory of Open Access Journals public dump (22 MB, downloaded 28/05/2023)", "[Data Used] ERIH\nT... |
null | null | null | dx.doi.org/10.17504/protocols.io.h57b89n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol for Immunohistochemistry free-floating sections with anti-doublecortin antibody for avian tissue.</p>
[STEPS]
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80,088 | DNA extraction (BOMB) | 4 | dx.doi.org/10.17504/protocols.io.n2bvj6mdnlk5/v4 | https://www.protocols.io/view/dna-extraction-bomb-csfywbpw | Tsu-Chun Hung, Yin-Tse Huang | TITLE: DNA extraction (BOMB)
AUTHORS: Tsu-Chun Hung, Yin-Tse Huang
[DESCRIPTION]
DNA extraction (BOMB)
[STEPS]
SECTION: Sample Collection
1. Add 200 µL of 1mm beads to 1.5mL eppendorf tube
SECTION: Sample Collection
2. Add200 µL of 0.5mm beads to 1.5mL eppendorf tube
SECTION: Sample Collection
3. Add870 µL Lysis ... | ["[Sample Collection] Add 200 µL of 1mm beads to 1.5mL eppendorf tube", "[Sample Collection] Add200 µL of 0.5mm beads to 1.5mL eppendorf tube", "[Sample Collection] Add870 µL Lysis master mix to 1.5mL eppendorf tube", "[Sample Collection] Collect 10-20 mg of sample to 1.5mL eppendorf tube", "[Sample crush] Put 1.5mL ep... |
98,708 | PCR and analysis | 0 | dx.doi.org/10.17504/protocols.io.kxygxypwdl8j/v1 | https://www.protocols.io/view/pcr-and-analysis-dcmu2u6w | Enrico Bagnoli, Miratul Muqit | TITLE: PCR and analysis
AUTHORS: Enrico Bagnoli, Miratul Muqit
[DESCRIPTION]
This protocol details the PCR analysis.
[STEPS]
SECTION: PCR setup
1.
Include at least two housekeeping control
SECTION: PCR setup
2.
Prepare a working solution at 10 micromolar (µM) by diluting 1:10 the stock in PCR-grade water.
... | ["[PCR setup] Include at least two housekeeping control", "[PCR setup] Prepare a working solution at 10 micromolar (µM) by diluting 1:10 the stock in PCR-grade water.", "[PCR setup] In each well of a 384 well-plate,5 µL of samples + master mix have to be added, according to the following volumes:\n\nDNA: 2 µL\nMasterMi... |
28,936 | RNA extraction from Pichia pastoris | null | dx.doi.org/10.17504/protocols.io.8hght3w | null | iGEM Dusseldorf | TITLE: RNA extraction from Pichia pastoris
AUTHORS: iGEM Dusseldorf
[STEPS]
?. pipeting hole culture of Pichia liquid culture into 1.5 mL microcentrifuge tubes
?. centrifugation for 1 min at 10.000 x g
?. discard the supernatant
?. extract RNA with Kit: for e.g. ZymoResearch YeaStar RNA Kit (Cat.#R1002) following t... | ["pipeting hole culture of Pichia liquid culture into 1.5 mL microcentrifuge tubes", "centrifugation for 1 min at 10.000 x g", "discard the supernatant", "extract RNA with Kit: for e.g. ZymoResearch YeaStar RNA Kit (Cat.#R1002) following the manufacturers manual.", "messure the concentration\na A260/280 ratio of ~2.0... |
59,989 | Detection and Quantification of Calcitonin Gene-Related Peptide in Human Blood Plasma using a Modified Enzyme-Linked Immunosorbent Assay | 1 | dx.doi.org/10.17504/protocols.io.3byl4b98jvo5/v2 | https://www.protocols.io/view/detection-and-quantification-of-calcitonin-gene-re-b6tvren6 | Pavan S. Krishnan, Fernando T. Zamuner, Carolyn M. Jenks, Yanjun Xie, Lisa Zhang, Mohammed Lehar, Marcos Iglesias , Neal S. Fedarko, Mariana Brait, John P. Carey | TITLE: Detection and Quantification of Calcitonin Gene-Related Peptide in Human Blood Plasma using a Modified Enzyme-Linked Immunosorbent Assay
AUTHORS: Pavan S. Krishnan, Fernando T. Zamuner, Carolyn M. Jenks, Yanjun Xie, Lisa Zhang, Mohammed Lehar, Marcos Iglesias , Neal S. Fedarko, Mariana Brait, John P. Carey
[DES... | ["[Sample Collection and Preparation] Collect whole blood from antecubital vein into 6.0 mL BD Vacutainer EDTA collection tube", "[Sample Collection and Preparation] Add 0.5 mL of aprotinin competitive serine protease inhibitor to tube after collection", "[Sample Collection and Preparation] Centrifuge at 3000 rpm for 4... |
29,356 | Effective and efficient cytoskeleton (actin and microtubules) fluorescence staining of adherent eukaryotic cells | 1 | dx.doi.org/10.17504/protocols.io.8wkhxcw | https://www.protocols.io/view/effective-and-efficient-cytoskeleton-actin-and-mic-8wkhxcw | Matthew Brown | TITLE: Effective and efficient cytoskeleton (actin and microtubules) fluorescence staining of adherent eukaryotic cells
AUTHORS: Matthew Brown
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Eukaryotic microbes, protists, are highly diverse organisms with complex cytoskeletal elements used for movem... | ["Move cells onto a chamber culture slide (Lab-Tek™ II Chamber Slide - Thermo Fisher Scientific - 154461) according to how the cells are being grown, see below.", "If cells are growing in liquid media in a tissue culture flask, scrap cells with a cell scraper to dislodge cells from tissue culture flask. Move 1 mL to ea... |
null | null | null | dx.doi.org/10.17504/protocols.io.iabcaan | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol provides an efficient DNA extraction and purification of historical museum hides, which potentially have been chemically tanned.</p>
[BEFORE_START]
<p>Clean</p>
[STEPS]
?.
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85,962 | shRNA knockdown | 4 | dx.doi.org/10.17504/protocols.io.e6nvwdjj7lmk/v1 | https://www.protocols.io/view/shrna-knockdown-cx7ixrke | wusj, Nancy C. Hernandez Villegas, schekman | TITLE: shRNA knockdown
AUTHORS: wusj, Nancy C. Hernandez Villegas, schekman
[DESCRIPTION]
This protocol describes a standard procedure to generate a stable cell line for a DNAJC5 knockdown using shRNA.
[STEPS]
SECTION: shRNA knockdown
2. plKO.1-Hygroplasmids-containing shRNA targeting DNAJC5 (ccggGCAACCTCAGATGACAT... | ["[shRNA knockdown] plKO.1-Hygroplasmids-containing shRNA targeting DNAJC5 (ccggGCAACCTCAGATGACATTAAACTCGAGTTTAATGTCATCTGAGGTTGCTTTTTG) together with pMD2.G and PsPAX2 were transfected into HEK293T cells to produce lentiviral particles for 72 hr.", "[shRNA knockdown] HEK293T cells were plated at a density such that on ... |
108,543 | The "Material and Methods" section of the manuscript entitled "The prognostic value of H3K27me3 implies potential therapeutic targets of EZH2 in sinonasal soft tissue sarcoma: evidence gained from a single-arm, prospective, observational trial | 0 | dx.doi.org/10.17504/protocols.io.yxmvmeq5bg3p/v2 | https://www.protocols.io/view/the-34-material-and-methods-34-section-of-the-manu-dm8749zn | Chengle Zhou, Jingyi Yang | TITLE: The "Material and Methods" section of the manuscript entitled "The prognostic value of H3K27me3 implies potential therapeutic targets of EZH2 in sinonasal soft tissue sarcoma: evidence gained from a single-arm, prospective, observational trial
AUTHORS: Chengle Zhou, Jingyi Yang
[DESCRIPTION]
The ma... | ["[7. Construction of Tissue microarrays] Whole slides staining of 27 formalin-fixed, paraffin-embedded (FFPE) tumor samples was firstly conducted utilizing available surgical specimen obtained from the observational trial cohort for primitive discovery. For subsequent validation, remaining FFPE specimens of the previo... |
42,058 | SHARE-seq V1 | 4 | dx.doi.org/10.17504/protocols.io.bmbik2ke | https://www.protocols.io/view/share-seq-v1-bmbik2ke | Sai Ma, Aviv Regev, Jason Buenrostro | TITLE: SHARE-seq V1
AUTHORS: Sai Ma, Aviv Regev, Jason Buenrostro
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">SHARE-seq for joint profiling of chromatin accessibility and gene expression at scale.</div></div>
[STEPS]
?. [Anneal oligo plates]
Dilute 120µl Round 1 linker oligo (1mM) with 11880µl... | ["[Anneal oligo plates]\nDilute 120µl Round 1 linker oligo (1mM) with 11880µl STE buffer. Mix 90µl diluted Round 1 linker oligo with 10µl Round 1 oligo (100µM) in a 96 well PCR plate.", "[Anneal oligo plates]\nDilute 120µl Round 2 linker oligo (1mM) with 9480µl STE buffer. Mix 88µl diluted Round 2 linker oligo with 12µ... |
108,198 | Pan-Cancer Analysis of the Prognostic and Immunological Roles of SHP-1/ptpn6 | 0 | dx.doi.org/10.17504/protocols.io.rm7vzjdpxlx1/v1 | https://www.protocols.io/view/pan-cancer-analysis-of-the-prognostic-and-immunolo-dmwe47be | Ping Cui, Jie Lian, Yang Liu, Dongsheng Zhang, Yao Lin, Lili Lu, Li Ye, Hui Chen, Sanqi An, Jiegang Huang, Hao Liang | TITLE: Pan-Cancer Analysis of the Prognostic and Immunological Roles of SHP-1/ptpn6
AUTHORS: Ping Cui, Jie Lian, Yang Liu, Dongsheng Zhang, Yao Lin, Lili Lu, Li Ye, Hui Chen, Sanqi An, Jiegang Huang, Hao Liang
[DESCRIPTION]
In this paper, we present a comprehensive analysis of ptpn6 across various cancers using multip... | ["[Protocal] Differential expression analysis \nThe Tumor Immune Estimation Resource (TIMER) 2.0 (http://timer.cistrome.org/) is an online website used to investigate the pan-cancer analysis of gene expression or correlation, and immune infiltration 1. Difference of ptpn6 expression between tumors and adjacent normal t... |
45,945 | Dishwasher | 4 | null | https://www.protocols.io/view/dishwasher-bq4zmyx6 | Elizabeth Fozo | TITLE: Dishwasher
AUTHORS: Elizabeth Fozo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Steris Dishwasher protocol</div><div class = "text-block">Steris corporation </div><div class = "text-block">Account manager/rep: LeenaAsplund</div><div class = "text-block"><span>Email: </span><a href="mailto:... | ["[Steris Dishwasher protocol]\nOpen door- bottom left button/door and up arrow graphic", "[Steris Dishwasher protocol]\nClose door- bottom left button/door and down arrow graphic", "[Steris Dishwasher protocol]\nView cycle, Select cycle, and Start cycle are all located on the operation screen", "[Steris Dishwasher pro... |
63,895 | Care Renew Blood Sugar Balance Reviews – Is CareRenew Legit or Scam? | 3 | dx.doi.org/10.17504/protocols.io.eq2lyn2owvx9/v1 | https://www.protocols.io/view/care-renew-blood-sugar-balance-reviews-is-carerene-camxsc7n | neeransheram | TITLE: Care Renew Blood Sugar Balance Reviews – Is CareRenew Legit or Scam?
AUTHORS: neeransheram
[DESCRIPTION]
Care Renew Blood Sugar Balance
[STEPS] | [] |
92,312 | Percutaneous myocardial infarction model in rabbit | 4 | dx.doi.org/10.17504/protocols.io.yxmvm3b39l3p/v1 | https://www.protocols.io/view/percutaneous-myocardial-infarction-model-in-rabbit-c6dyza7w | Eline Huethorst, Michael Freeman, Erin Boland, Michael Dunne, Francis Burton, Chris Denning, Rachel Myles, Godfrey Smith | TITLE: Percutaneous myocardial infarction model in rabbit
AUTHORS: Eline Huethorst, Michael Freeman, Erin Boland, Michael Dunne, Francis Burton, Chris Denning, Rachel Myles, Godfrey Smith
[DESCRIPTION]
This video file contains fluoroscopic recordings of 6 steps of the percutaneous inductions of myocardial infarction i... | [] |
57,427 | protein extraction from cell pallets | 1 | dx.doi.org/10.17504/protocols.io.b4btqsnn | https://www.protocols.io/view/protein-extraction-from-cell-pallets-b4btqsnn | Jacob Waldbauer, Lichun Zhang, Jacob Waldbauer, Lichun Zhang | TITLE: protein extraction from cell pallets
AUTHORS: Jacob Waldbauer, Lichun Zhang, Jacob Waldbauer, Lichun Zhang
[DESCRIPTION]
Use LDS buffer to extract protein from cell palllets
[STEPS]
1. Make 1X LDS buffer. In 40mL of 1X buffer, add Tris HCl 0.666g, Tris base 0.682g, LDS 0.8g, EDTA 0.006g, Glycerol 4g.
2. ... | ["Make 1X LDS buffer. In 40mL of 1X buffer, add Tris HCl 0.666g, Tris base 0.682g, LDS 0.8g, EDTA 0.006g, Glycerol 4g.", "make 1M DTT stock solution in LC/MS water.", "Add 200~500uL of 10mM DTT in 1X LDS buffer to the cell pallet tube.", "Heat sample up at 95ºC for 20 minutes.", "Cool down the sample to room temrature.... |
24,369 | CGAP Human Spleen Dissociation, Tissue Stability Study | null | dx.doi.org/10.17504/protocols.io.32rgqd6 | null | Anna Wilbrey-Clark, Adam Hunter | TITLE: CGAP Human Spleen Dissociation, Tissue Stability Study
AUTHORS: Anna Wilbrey-Clark, Adam Hunter
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Mechanical dissociation of human spleen tissue to single cells for use in 10X chromium scRNA-Seq preparation. </div></div>
[STEPS]
?. Receive spleen... | ["Receive spleen punch in hypothermasol FRS (Sigma H4416) solution.", "Place spleen punch onto 100mm Glass Petri Dish.", "Add 10ml Cold PBS.", "Slice spleen punch into pieces (less than 10x10x10mm).", "Transfer spleen pieces and PBS into 50ml Falcon Tube.", "Add 100µl DNAse I dropwise to spleen punch in PBS to a final ... |
null | null | null | dx.doi.org/10.17504/protocols.io.e36bgre | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>Immunochemistry Protocols: Immunopurification ‐ (Small Scale) Using Anti‐Epitope Tag Affinity Matrices:</strong></p>
<p> </p>
<p>Typically, immunoprecipitation of antigen from extracts of transfected mammalian cells requires between 1-5 μL of polyclonal antiserum, 5-1... | [] |
55,502 | 2,4-dinitrophenylhydrazine alpha-ketoglutarate detection assay for Prolyl Hydroxylase Domain (PHD) proteins | 4 | null | https://www.protocols.io/view/2-4-dinitrophenylhydrazine-alpha-ketoglutarate-det-b2fnqbme | sjwong | TITLE: 2,4-dinitrophenylhydrazine alpha-ketoglutarate detection assay for Prolyl Hydroxylase Domain (PHD) proteins
AUTHORS: sjwong
[DESCRIPTION]
The 2,4-dinitrophenylhydrazine (2,4-DNPH) alpha-ketoglutarate detection assay was developed to support the study of prolyl hydroxylase domain (PHD) proteins in a substrate-... | ["[In vitro hydroxylation assay] Prepare 5 Eppendorf tubes containing 50 µl of 10% TCA.\nLabel tubes: 0 min, 1 min, 2 min, 5 min, 15 min.", "[In vitro hydroxylation assay] Prepare cofactor solution containing HEPES/MES, catalase, DTT, ascorbic acid, FeSO4, a-ketoglutarate, and peptide in a 150 µl volume in an Eppendorf... |
71,926 | Midbrain organoid astrocyte seeding | 4 | dx.doi.org/10.17504/protocols.io.rm7vzbyp4vx1/v1 | https://www.protocols.io/view/midbrain-organoid-astrocyte-seeding-cigwubxe | gustavo.parfitt | TITLE: Midbrain organoid astrocyte seeding
AUTHORS: gustavo.parfitt
[DESCRIPTION]
Midbrain organoid astrocyte seeding protocol
[STEPS]
1. Refer to the publish protocols to obtain the cell materials required.
https://www.protocols.io/view/midbrain-organoid-differentiation-in-spinner-flask-rm7vzbnr4vx1/v1
https://www.... | ["Refer to the publish protocols to obtain the cell materials required.\nhttps://www.protocols.io/view/midbrain-organoid-differentiation-in-spinner-flask-rm7vzbnr4vx1/v1\nhttps://www.protocols.io/view/astrocyte-extraction-from-brain-organoids-261ge364wl47/v2", "From a 90% confluent plate of astrocytes.", "Wash with PBS... |
94,223 | Y-Maze Protocol | 4 | dx.doi.org/10.17504/protocols.io.eq2lyjr1mlx9/v1 | https://www.protocols.io/view/y-maze-protocol-c79pzr5n | Lisa Blackmer-Raynolds, Ian N Krout, Tim Sampson | TITLE: Y-Maze Protocol
AUTHORS: Lisa Blackmer-Raynolds, Ian N Krout, Tim Sampson
[DESCRIPTION]
The Y maze is a quick and easy way to evaluate a rodent’s spatial working memory by measuring their ability to effectively explore a Y shape maze. Rodents typically prefer to explore novel arms of the maze, rather than retur... | ["[Methods] Bring mice up to the behavior room to acclimate at least 60 min before testing.", "[Methods] Clean each maze with 70% ethanol and let dry before beginning each test.", "[Methods] Start Ethovision recording before placing rodents in center of maze (if you have multiple Y mazes, you can run cage mates simulta... |
null | null | null | dx.doi.org/10.17504/protocols.io.e8tbhwn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?. | [] |
93,162 | 0.1xBWT buffer | 3 | dx.doi.org/10.17504/protocols.io.e6nvwdnn7lmk/v1 | https://www.protocols.io/view/0-1xbwt-buffer-c68izhue | Anna Schmidt, Sarah Nagel, Matthias Meyer | TITLE: 0.1xBWT buffer
AUTHORS: Anna Schmidt, Sarah Nagel, Matthias Meyer
[DESCRIPTION]
Protocol for the preparation of 0.1x BWT buffer (Wash buffer II) for automated single-stranded DNA library preparation using the ssDNA2.0 method (Gansauge et al. 2020).
References
Gansauge, M.-T., Aximu-Petri, A., Nagel, S., & Meye... | [] |
58,697 | Immunofluorescence-based assay to assess LRRK2 association with microtubules in HEK293 cells | 4 | dx.doi.org/10.17504/protocols.io.b5jhq4j6 | https://www.protocols.io/view/immunofluorescence-based-assay-to-assess-lrrk2-ass-b5jhq4j6 | Elena Purlyte, Alexia Kalogeropulou, Francesca Tonelli , Dario R Alessi | TITLE: Immunofluorescence-based assay to assess LRRK2 association with microtubules in HEK293 cells
AUTHORS: Elena Purlyte, Alexia Kalogeropulou, Francesca Tonelli , Dario R Alessi
[DESCRIPTION]
Previous studies using confocal fluorescence microscopy and cryo-electron microscopy reported that most pathogenic LRRK2 m... | ["[Reverse transfection of HEK293 cells] Prepare a transfection mix by adding 0.6 µg of Flag-LRRK2 (or Flag-empty vector) cDNA and 1.8 µL of 1 mg/mL PEI solution into 150 µL of Opti-MEM for each well. Vortex for 20 s/30 s.", "[Reverse transfection of HEK293 cells] Incubate the transfection mix for 20 min at Room temper... |
100,888 | Nuclei Isolation from Flash Frozen Intestinal Tissue | 0 | null | https://www.protocols.io/view/nuclei-isolation-from-flash-frozen-intestinal-tiss-dery3d7w | Caden Sweet, mimeyer, Scott Magness | TITLE: Nuclei Isolation from Flash Frozen Intestinal Tissue
AUTHORS: Caden Sweet, mimeyer, Scott Magness
[DESCRIPTION]
This protocol is for isolating, fixing, and freezing nuclei from flash frozen human intestinal full thickness samples for single nucleus RNA sequencing. Adapted from Invent Biotech Minute Detergent-Fr... | ["[Obtain Reagents Before Starting]", "[Methods] Thaw a Mr. Frosty freezing container at room temperature, or fill up to line with Isopropanol.", "[Methods] Cool centrifuge to 4°C.", "[Methods] Follow Parse fixation protocol for coating 15 mL conicals in 1% BSA prior to starting. Coat 2 conicals per sample you’re isola... |
101,261 | KAPP-Sen TMC: Tissue Section Preparation and H&E Staining | 1 | dx.doi.org/10.17504/protocols.io.dm6gpzzkjlzp/v1 | https://www.protocols.io/view/kapp-sen-tmc-tissue-section-preparation-and-h-amp-de5m3g46 | Juliana Alcoforado Diniz, Ramalakshmi Ramasamy, Paul Robson, Elaine Bechtel | TITLE: KAPP-Sen TMC: Tissue Section Preparation and H&E Staining
AUTHORS: Juliana Alcoforado Diniz, Ramalakshmi Ramasamy, Paul Robson, Elaine Bechtel
[DESCRIPTION]
Before performing further spatial transcriptomic analysis, FFPE blocks were submitted to hematoxylin and eosin stain. All these procedures were perform... | ["[Preparation of the Workspace] Prepare workspace according to https://dx.doi.org/10.17504/protocols.io.36wgq37polk5/v1", "[Routine H&E Protocol: Leica AutoStainer XL] Step\n \n \n Station\n \n \n Reagent\n \n \n Time\n \n \n Exact\n \n \n \n 1\n \n \n 1\n \n \n Xylene\n \n \n 3:00\n \n ... |
28,032 | Decreased risk of Parkinson’s disease in diabetic patients with thiazolidinediones therapy: An exploratory meta-analysis | null | dx.doi.org/10.17504/protocols.io.7k8hkzw | null | Yueli Zhu, Jiali Pu, Yanxing Chen, Baorong Zhang | TITLE: Decreased risk of Parkinson’s disease in diabetic patients with thiazolidinediones therapy: An exploratory meta-analysis
AUTHORS: Yueli Zhu, Jiali Pu, Yanxing Chen, Baorong Zhang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Parkinson’s disease (PD) is a prevalent and complex neurodeg... | [] |
22,375 | Electrochemical Gradients Assessment Device (EGAD) | null | dx.doi.org/10.17504/protocols.io.z4ff8tn | null | Jack Cerchiara, Kerry Kim, Eli Meir, Mary Pat Wenderoth, Jennifer H. Doherty | TITLE: Electrochemical Gradients Assessment Device (EGAD)
AUTHORS: Jack Cerchiara, Kerry Kim, Eli Meir, Mary Pat Wenderoth, Jennifer H. Doherty
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The basis for understanding neurophysiology is understanding ion movement across cell membranes. Stude... | [] |
82,296 | TSST | 1 | dx.doi.org/10.17504/protocols.io.e6nvwj85zlmk/v2 | https://www.protocols.io/view/tsst-cukywuxw | Johannes Bodo Heekerens | TITLE: TSST
AUTHORS: Johannes Bodo Heekerens
[DESCRIPTION]
This protocol details about Trier Social Stress Test (TSST).
[GUIDELINES]
Instructions for investigators (German)
Vor dem TSST (Raum A)
Vor dem TSST zeigt und erklärt der Versuchsleiter dem Probanden die drei mobilen Geräte zur kontinuierlichen Erfassung v... | ["[Before the TSST] Before the TSST, the investigator shows and explains to the subject the devices for the assessment of heart rate (Vivalink ECG Patch), electrodermal activity (Empatica Smartwatch), and blood pressure (iHealth BP Cuff). The subject is instructed to put the devices on. The investigator makes sure that... |
null | null | null | dx.doi.org/10.17504/protocols.io.ipgcdjw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The four SNPs (C5178A, A10398G, G13708A, and C13928G) in the mtDNA coding region were detected using PCR-RFLP analysis. The primers listed in able 2 were used to amplify target fragments. The mismatch method was applied to generate an HpyCH4Ⅲ artificial restriction endonuclea... | [] |
78,066 | Bulk RNA sequencing | 4 | dx.doi.org/10.17504/protocols.io.36wgqjqbkvk5/v1 | https://www.protocols.io/view/bulk-rna-sequencing-cqgsvtwe | anita.adami | TITLE: Bulk RNA sequencing
AUTHORS: anita.adami
[DESCRIPTION]
This protocol describes how to perform bulk RNA sequencing
[STEPS]
SECTION: Bulk RNA sequencing
1. Total RNA was isolated from nuclei (Nuclear Extraction from Tissue for FACS), cell culture samples, or tissue using the RNeasy Mini Kit (Qiagen).
SECTION: Bu... | ["[Bulk RNA sequencing] Total RNA was isolated from nuclei (Nuclear Extraction from Tissue for FACS), cell culture samples, or tissue using the RNeasy Mini Kit (Qiagen).", "[Bulk RNA sequencing] Libraries were generated using Illumina TruSeq Stranded mRNA library prep kit (poly-A selection) and sequenced on a NextSeq50... |
53,121 | Optimization of ROS measurement and localization in plant tissues: challenges and solutions | 4 | dx.doi.org/10.17504/protocols.io.bx49pqz6 | https://www.protocols.io/view/optimization-of-ros-measurement-and-localization-i-bx49pqz6 | taras.p.pasternak , Jose Manuel Perez-Perez | TITLE: Optimization of ROS measurement and localization in plant tissues: challenges and solutions
AUTHORS: taras.p.pasternak , Jose Manuel Perez-Perez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">During the last decade, there has been a huge inter... | ["[H2O2 quantification with DCHBS/AAP method. ]\nStep 1. For tissue pre-adaptation, transfer your seedlings, cells, or tissue explants to a 40 mm round Petri plate containing 3-4 ml of the physiologically-balanced plant growth medium (e.g., TK1 for Arabidopsis or TK4 for tobacco) and incubate them for at least 4 h in t... |
103,195 | Postnatal astrocyte labeling by electroporation (PALE) | 0 | dx.doi.org/10.17504/protocols.io.eq2lyweprvx9/v1 | https://www.protocols.io/view/postnatal-astrocyte-labeling-by-electroporation-pa-dgz33x8n | Shiyi Wang | TITLE: Postnatal astrocyte labeling by electroporation (PALE)
AUTHORS: Shiyi Wang
[DESCRIPTION]
Postnatal astrocyte labeling by electroporation (PALE)
[STEPS]
1. **Animal Preparation**
1.1. - Sedate late P0/early P1 mice by hypothermia until anesthetized.
2. **Plasmid Preparation**
2.1. - Prepare plasmid DNA mixed wi... | ["**Animal Preparation**", "- Sedate late P0/early P1 mice by hypothermia until anesthetized.", "**Plasmid Preparation**", "- Prepare plasmid DNA mixed with Fast Green Dye for visualization.", "**Injection Procedure**", "- Inject 1 μl of plasmid DNA mixture into the lateral ventricle of one hemisphere using a pulled gl... |
44,825 | Challenge Assay | 4 | null | https://www.protocols.io/view/challenge-assay-bpzzmp76 | Elizabeth Fozo | TITLE: Challenge Assay
AUTHORS: Elizabeth Fozo
[STEPS]
?. [Challenge Assay]
Have plenty of BHI plates ready. Calculate the number of plates you will need for dilutions (if you expect more killing for a certain strain/condition/time point, dilutions will be lower), label plates accordingly.
?. [Challenge Assay]
Prepare... | ["[Challenge Assay]\nHave plenty of BHI plates ready. Calculate the number of plates you will need for dilutions (if you expect more killing for a certain strain/condition/time point, dilutions will be lower), label plates accordingly.", "[Challenge Assay]\nPrepare plenty of tubes for serial dilutions. Make a solution ... |
81,857 | Optimising sample multiplexing oligos by flow cytometry | 4 | dx.doi.org/10.17504/protocols.io.81wgbyjpovpk/v1 | https://www.protocols.io/view/optimising-sample-multiplexing-oligos-by-flow-cyto-ct69wrh6 | Daniel V Brown | TITLE: Optimising sample multiplexing oligos by flow cytometry
AUTHORS: Daniel V Brown
[DESCRIPTION]
Optmisation of sample multiplexing oligos by scRNA-Seq is costly and time consuming. A cheaper and faster method is to use a flow cytometry read-out with fluorescent detection oligonucleotides.
This method can also be ... | ["[MULTI-Seq oligo preparation] Mix anchor and barcode strands in 1:1 molar ratio in PBS (without FBS or BSA at 2 µM concentration (10X stock).", "[MULTI-Seq oligo preparation] This is 6uL 50uM anchor LMO, and 15uL 10uM barcode oligo to 129uL plain PBS.", "[MULTI-Seq oligo preparation] Make one unique barcode solution ... |
83,503 | Endosome isolation | 1 | dx.doi.org/10.17504/protocols.io.14egn3bp6l5d/v1 | https://www.protocols.click/view/endosome-isolation-cvspw6dn | Chuyu Chen | TITLE: Endosome isolation
AUTHORS: Chuyu Chen
[DESCRIPTION]
Subcellular fractionation to isolate early and late endosomes (EEs and LEs) by performing a series of centrifugation steps.
[STEPS]
SECTION: Continuous sucrose gradient tube preparation
7. add 2.5 ml 0.45M sucrose on top of frozen buffer S3 and wait for 10 ... | ["[Continuous sucrose gradient tube preparation] add 2.5 ml 0.45M sucrose on top of frozen buffer S3 and wait for 10 min or until it frozen", "[Continuous sucrose gradient tube preparation] keep the frozen tubes at -80 until experiment day", "[Continuous sucrose gradient tube preparation] prepare 0.5M and 2M sucrose bu... |
null | null | null | dx.doi.org/10.17504/protocols.io.ss2eege | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is used to clarity the process of the mate-pair large libraries preparation for the L. maculatus.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?. | [] |
39,928 | MirVana RNA | 3 | dx.doi.org/10.17504/protocols.io.bi8ykhxw | https://www.protocols.io/view/mirvana-rna-bi8ykhxw | John E Gorzynski | TITLE: MirVana RNA
AUTHORS: John E Gorzynski
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.hh4b38w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol we have used for the electroporation of mRNA encoding reporter gene Lucipherase into following organisms: <em>Chromera velia</em>, <em>Alexandrium minutum</em>, <em>Euglena gracilis</em>, <em>Pyramimonas parkease</em>, <em>Pyramimonas orientalis</em><em>, Eutrep... | [] |
40,836 | Study Procedures (Part 6 of Phase 3 study of Vaccine Candidate for COVID-19) | 1 | dx.doi.org/10.17504/protocols.io.bj5ckq2w | https://www.protocols.io/view/study-procedures-part-6-of-phase-3-study-of-vaccin-bj5ckq2w | Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores | TITLE: Study Procedures (Part 6 of Phase 3 study of Vaccine Candidate for COVID-19)
AUTHORS: Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This is part 6 of: "Phase 3 randomized, double-blinded, placebo-controlled trial to evaluate the s... | ["[Screening visit: to Day 0 (Study procedures and evaluation)]\nAfter the site PI has obtained informed consent from participants, several procedures will be completed during screening to determine study eligibility. Baseline data will be collected during screening between seven days prior to first vaccination and o... |
107,618 | Transcardial Perfusion in Mice for Synaptic Evaluation and QUantification by Imaging Nanostructure (SEQUIN) Analysis | 4 | dx.doi.org/10.17504/protocols.io.36wgqnk85gk5/v1 | https://www.protocols.io/view/transcardial-perfusion-in-mice-for-synaptic-evalua-dmca42se | Saroj Kumar Sah, Thomas Biederer | TITLE: Transcardial Perfusion in Mice for Synaptic Evaluation and QUantification by Imaging Nanostructure (SEQUIN) Analysis
AUTHORS: Saroj Kumar Sah, Thomas Biederer
[DESCRIPTION]
This protocol details the method for transcardial perfusion in mice for Synaptic Evaluation and QUantification by Imaging Nanostructure (SE... | ["[Transcardial Perfusion] Make a mixture of ketamine (100 mg/kg) and xylazine (10 mg/kg), sufficient to anesthetize all mice.", "[Transcardial Perfusion] Administer anesthesia to one mouse via intraperitoneal injection and place it in a clean cage until the anesthesia takes effect. Perform a firm toe pinch to ensure t... |
99,676 | Automated eDNA Extraction from Estuarine Samples Using Magnetic Beads | 0 | dx.doi.org/10.17504/protocols.io.5jyl82jn9l2w/v1 | https://www.protocols.io/view/automated-edna-extraction-from-estuarine-samples-u-ddj424qw | Fouad El Baidouri , Muriel Kelly, Heather L. Gilbert, Alison Watts | TITLE: Automated eDNA Extraction from Estuarine Samples Using Magnetic Beads
AUTHORS: Fouad El Baidouri , Muriel Kelly, Heather L. Gilbert, Alison Watts
[DESCRIPTION]
This method presents an optimized protocol for the automated extraction of environmental DNA (eDNA) from estuarine samples using magnetic beads. The add... | ["[Sample Preparation] Perform the following steps in a biosafety cabinet under aseptic conditions\nFor samples collected on filters stored in Longmire's buffer (wet filters)\nPipette out all of the Longmire's buffer from the sample tube into a separate Eppendorf tube (leave the sample filter in the sample tube)\nPipet... |
62,072 | Highly Parallel Droplet Sample Preparation for Single Cell Proteomics | 1 | dx.doi.org/10.17504/protocols.io.4r3l24r7qg1y/v3 | https://www.protocols.io/view/highly-parallel-droplet-sample-preparation-for-sin-b8uyrwxw | Andrew Leduc, Richard Huffman, Joshua Cantlon, Saad Khan, Nikolai Slavov | TITLE: Highly Parallel Droplet Sample Preparation for Single Cell Proteomics
AUTHORS: Andrew Leduc, Richard Huffman, Joshua Cantlon, Saad Khan, Nikolai Slavov
[DESCRIPTION]
Protocol for preparing single cells for mass-spec analysis by nPOP as described by Leduc et al., 2021, 2022 DOI: 10.1186/s13059-022-02817-5. nPOP ... | ["[Setting up system] This protocol enables highly paralleled single cell sample prep for that can be used for label free analysis but has most utility for multiplexed analysis. \n\nWe provide options for TMT 18 plex with carrier (14plex) and mTRAQ labels for multiplexed DIA analysis (2plex or 3plex). \n\nWhich option ... |
98,450 | SenNet Case Selection Protocol | JHU TMC | 0 | dx.doi.org/10.17504/protocols.io.q26g71z1kgwz/v2 | https://www.protocols.io/view/sennet-case-selection-protocol-jhu-tmc-dcds2s6e | Kyu Sang Han, Fan Wu, Sashank Reddy, Denis Wirtz, Joel Sunshine, Pei-Hsun Wu | TITLE: SenNet Case Selection Protocol | JHU TMC
AUTHORS: Kyu Sang Han, Fan Wu, Sashank Reddy, Denis Wirtz, Joel Sunshine, Pei-Hsun Wu
[DESCRIPTION]
Inclusion
Age below 30 or above 50.
English Speaking.
Able to provide consent.
Resected pancreas tissue.
Clear and normal
structured islets of Langerhans, acinus, and duct... | ["[Disclaimer] Patient samples will be obtained from distal pancreatectomy, splenectomy, and cholecystectomy. No other procedures or follow-up is needed for research purposes.", "[Inclusion] Age below 30 or above 50.\nEnglish Speaking.\nAble to provide consent.\nResected pancreas tissue.\nClear and normal structured is... |
65,563 | Nucleofection and single-cell cloning of CRISPR KO clones | 4 | dx.doi.org/10.17504/protocols.io.n2bvj61wwlk5/v1 | https://www.protocols.io/view/nucleofection-and-single-cell-cloning-of-crispr-ko-cb93sr8n | Goran Tomic | TITLE: Nucleofection and single-cell cloning of CRISPR KO clones
AUTHORS: Goran Tomic
[DESCRIPTION]
This protocol describes the process of nucleofection of sgRNA in PX458 plasmid into a mouse cancer cell line and subsequent flow sorting of single cells based on GFP fluorescence.
[BEFORE_START]
If the cell line is n... | ["Following sgRNA cloning into PX458 plasmid (Cas9-2A-GFP), the plasmid can be introduced into the cells by nucleofection. I use Nucleofector 2b device.", "Trypsinise cells on 70-90% 10 cm plate. Count and spin down 1.5-2 x 10^6 cells per reaction (3 min, 1200 rpm). Switch on the Nucleofector device and set to the pred... |
80,365 | Spectrophotometric Quantification of Betacyanins in Plant Tissue Produced from the RUBY Reporter Gene | 4 | dx.doi.org/10.17504/protocols.io.3byl4j4xrlo5/v1 | https://www.protocols.io/view/spectrophotometric-quantification-of-betacyanins-i-csqmwdu6 | matthew.morgan | TITLE: Spectrophotometric Quantification of Betacyanins in Plant Tissue Produced from the RUBY Reporter Gene
AUTHORS: matthew.morgan
[DESCRIPTION]
RUBY is a visual reporter gene that produces beatnin, a betacyanin that appears red to violet in colour (He et al., 2020). To assay betanin (and other betalains) a spectrop... | ["[Sample Preparation] Take 20-50 mg of frozen tissue and add to 2 ml tubes. Keep on ice.", "[Sample Preparation] Grind down tissue using plastic micro-pestle and add methanol buffer (50% methanol, 1 mM ascorbic acid, 0.5% formic acid) at 10% w/v - i.e. for 35 mg of tissue add 350 ul methanol buffer.", "[Sample Prepara... |
98,607 | Differentiation of hPSCs into Dopamine neurons | 0 | dx.doi.org/10.17504/protocols.io.q26g71849gwz/v1 | https://www.protocols.io/view/differentiation-of-hpscs-into-dopamine-neurons-dcip2udn | Beatrice Weykopf | TITLE: Differentiation of hPSCs into Dopamine neurons
AUTHORS: Beatrice Weykopf
[DESCRIPTION]
This protocol describes the differentiation of hPSCs into dopaminergic neurons modified from Kriks et al., 2011 and Ryan et al., 2013
[STEPS]
1. Day -1: seed 200K cell/cm2 in mTeSR+ medium supplemented with 10µM Rock inhibit... | ["Day -1: seed 200K cell/cm2 in mTeSR+ medium supplemented with 10µM Rock inhibitor (RI) onto Martigel coated TC plates", "Day 0: Differentiation initiation. Aspirate mTeSR+ medium and add SRM media supplemented with 200nM LDN193189 + 10µM SB431542", "Day 1: SRM + LDN + SB supplemented with 100 ng/ml FGF8b, 100 ng/ml S... |
70,218 | DNA extraction for fermented plant based foods | 4 | dx.doi.org/10.17504/protocols.io.36wgqj9wkvk5/v1 | https://www.protocols.io/view/dna-extraction-for-fermented-plant-based-foods-cgtitwke | Anique Ahmad, Arya Gautam, Tsedenia Denekew, Ahmed Shibl, Aashish Jha | TITLE: DNA extraction for fermented plant based foods
AUTHORS: Anique Ahmad, Arya Gautam, Tsedenia Denekew, Ahmed Shibl, Aashish Jha
[DESCRIPTION]
DNA Extraction for fermented plant based foods
[BEFORE_START]
Label the following:
ZR BashingBeadTM Lysis Tubes (0.1 & 0.5 mm)
ZymoSpinTM III-F Filter in Collectio... | ["Secure in a Omni Bead Ruptor Elite bead beater fitted with a 2 ml tube holder assembly and process at max speed (30 m/s) for 5 min . Rest for 5 min .", "Centrifuge the ZR BashingBead™ Lysis Tubes (0.1 & 0.5 mm) in a microcentrifuge at ≥ 10000 x g, 1 min.", "Transfer up to 600 µL supernatant to the Zymo-Spin™ III-F Fi... |
null | null | null | dx.doi.org/10.17504/protocols.io.s7yehpw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
44,856 | High resolution negative silicone rubber impressions of perforation on stone personal elements for technological studies | 1 | dx.doi.org/10.17504/protocols.io.bp2ymqfw | https://www.protocols.io/view/high-resolution-negative-silicone-rubber-impressio-bp2ymqfw | Stefano Viola, Matteo Gios, Umberto Tecchiati, Stefano Viola | TITLE: High resolution negative silicone rubber impressions of perforation on stone personal elements for technological studies
AUTHORS: Stefano Viola, Matteo Gios, Umberto Tecchiati, Stefano Viola
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify">Al... | ["[Preliminary evaluation]\nEvaluation phase\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\tCareful evaluation of the degree of porosity and fragility of the object involved in the mold-making... |
24,460 | Electroporation of Caecitellus sp. with FITC-dextran | null | dx.doi.org/10.17504/protocols.io.35kgq4w | null | Nick Irwin, Elisabeth Hehenberger, Patrick Keeling | TITLE: Electroporation of Caecitellus sp. with FITC-dextran
AUTHORS: Nick Irwin, Elisabeth Hehenberger, Patrick Keeling
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-style:italic;">Caecitellus </span><span>sp.</span><span style = "font-weight:bold;"> </span><span>is a small pha... | ["[Culturing]\nCells were grown in f/2 media in a 20 C incubator on a 12:12 light:dark cycle.Cells fed on natural populations of bacteria in the culture and did not need supplemental food.", "[Electroporation]\nSpin down cells at 3000 x g for 10 minutes.Resuspend cells in 100 uL of BioRad Gene Pulser electroporation bu... |
34,788 | DNA metabarcoding protocol for siphonophore gut contents | 1 | dx.doi.org/10.17504/protocols.io.bd8ci9sw | https://www.protocols.io/view/dna-metabarcoding-protocol-for-siphonophore-gut-co-bd8ci9sw | Alejandro Damian Serrano | TITLE: DNA metabarcoding protocol for siphonophore gut contents
AUTHORS: Alejandro Damian Serrano
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">Protocol for the SiphWeb DNA metabarcoding of siphonophore gut content. </div></div><div class = "text-bl... | ["[DNA Extractionion]\nMainly identical to:http://www.bea.ki.se/documents/EN-DNeasy%20handbook.pdfWith the following modifications:-Digestion at -Elution using 2 rounds of incubation adn centrifuge with , incubating at , to a total of -Label Eppendorf tubes to hold the extracted DNA. Include the extraction number, ... |
90,000 | Husbandry guidelines for the safe brumation of two lacertid lizard species (Iberolacerta monticola and Podarcis lusitanicus) in laboratory conditions | 4 | dx.doi.org/10.17504/protocols.io.5jyl8p1p9g2w/v2 | https://www.protocols.io/view/husbandry-guidelines-for-the-safe-brumation-of-two-c35qyq5w | Frederico M Barroso | TITLE: Husbandry guidelines for the safe brumation of two lacertid lizard species (Iberolacerta monticola and Podarcis lusitanicus) in laboratory conditions
AUTHORS: Frederico M Barroso
[DESCRIPTION]
Lacertid lizards are often used for a range of laboratory studies in reptile behaviour, physiology, ecology etc. Howeve... | [] |
49,505 | MEDI: Macronutrient Extraction and Determination from Invertebrates | 6 | dx.doi.org/10.17504/protocols.io.buj9nur6 | https://www.protocols.io/view/medi-macronutrient-extraction-and-determination-fr-buj9nur6 | Jordan Cuff, Shawn M. Wilder | TITLE: MEDI: Macronutrient Extraction and Determination from Invertebrates
AUTHORS: Jordan Cuff, Shawn M. Wilder
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Macronutrients, comprising carbohydrates, proteins and lipids, underpin many ecological processes, but their quantification in ecological s... | ["[Collection and preparation of materials]\nCollect invertebrates and kill them, ideally by freezing.\nIf working with fluid-preserved specimens (e.g. alcohol-fixed), transfer all material including preserving agent into a suitable tube (e.g. 1.5 ml microcentrifuge tube or 2 ml screw-top collection tube) and evaporate... |
65,232 | Determination of MIC according to the EUCAST E.DEF 11.0 method | 4 | dx.doi.org/10.17504/protocols.io.kxygxz83kv8j/v1 | https://www.protocols.io/view/determination-of-mic-according-to-the-eucast-e-def-cbxqspmw | Khalid El Moussaoui | TITLE: Determination of MIC according to the EUCAST E.DEF 11.0 method
AUTHORS: Khalid El Moussaoui
[DESCRIPTION]
Determination of MIC according to the EUCAST E.DEF 11.0 method.
[STEPS]
1. With the disinfected tweezers, remove the filter (attention: do not take the filters of protections having a slightly bluer tint)... | ["With the disinfected tweezers, remove the filter (attention: do not take the filters of protections having a slightly bluer tint) and place them in the support provided for this purpose. Close the holder.", "Pour the contents of TUBE A (sterile water + Tween) onto the Petri dish containing the starting sample and wip... |
36,913 | Screening and Detection SARS-CoV-2 RNA from Buffy Coats | null | dx.doi.org/10.17504/protocols.io.bgarjsd6 | https://www.protocols.io/view/screening-and-detection-sars-cov-2-rna-from-buffy-bgarjsd6 | Mahesh Bachu, Bikash Mishra, Marie-Dominique Ah Kioon, Chaudhary Vidyanath | TITLE: Screening and Detection SARS-CoV-2 RNA from Buffy Coats
AUTHORS: Mahesh Bachu, Bikash Mishra, Marie-Dominique Ah Kioon, Chaudhary Vidyanath
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This SOP has been developed to minimize or eliminate employee occupational exposure to SARS-CoV-2... | ["Transfer the buffy bag from a sealed NYBC container to a BSL2 hood. Decontaminate the surface of the bag by spraying generous amount of 70% Ethanol. Using a 21 or 22 gauge needle fitted on a 5-10 ml syringe carefully collect ~100 - 200 µl of blood by carefully puncturing the top of the tubing of buffy bag.", "Erythro... |
null | null | null | dx.doi.org/10.17504/protocols.io.rszd6f6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div>
<p>A real-time RT-PCR targeting the 5' untranslated region of Yellow fever virus.</p>
<p>This protocol was designed and developed at this laboratory.</p>
</div>
[GUIDELINES]
<ul>
<li>If using a different brand or model of real-time thermocycler, check the concentration of... | [] |
41,217 | Effect of offering Phenylketonuria (PKU) mice Glycomacropeptide (GMP) before normal or low protein (LP) diet on growth, serum-phenylalanine (phe)-concentration, bone structure, performance and concentration of phe in the brain. | 1 | dx.doi.org/10.17504/protocols.io.bkg9ktz6 | https://www.protocols.io/view/effect-of-offering-phenylketonuria-pku-mice-glycom-bkg9ktz6 | kirsten.ahring , Mads Kjolby Department Of Biomedicine | TITLE: Effect of offering Phenylketonuria (PKU) mice Glycomacropeptide (GMP) before normal or low protein (LP) diet on growth, serum-phenylalanine (phe)-concentration, bone structure, performance and concentration of phe in the brain.
AUTHORS: kirsten.ahring , Mads Kjolby Department Of Biomedicine
[DESCRIPTION]
In... | ["[Protocol for mouse study] Project manager: Kirsten Ahring \n\nAdvisor: Frederik Dagnæs-Hansen\n\nProject title:Effect of offering Phenylketonuria (PKU) mice Glycomacropeptide (GMP) before normal or low \nprotein (LP) diet on growth, serum-phenylalanine (phe)-concentration, bone structure, performance and \nconcentra... |
null | null | null | dx.doi.org/10.17504/protocols.io.c7wzpd | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<strong>Purpose:</strong> to determine the concentration of DNA-containing particles in a given sample; useful in finding cell counts or phage titers.<br /><br />
[GUIDELINES]
<strong>Materials:<br /></strong><br />- 0.02 µm pore size, 25 mm diameter Anodisc filter... | [] |
77,391 | Split Luciferase Binding Assay (SLBA) Protocol | 4 | dx.doi.org/10.17504/protocols.io.4r3l27b9pg1y/v1 | https://www.protocols.io/view/split-luciferase-binding-assay-slba-protocol-cptpvnmn | Elzerackaityte, joe | TITLE: Split Luciferase Binding Assay (SLBA) Protocol
AUTHORS: Elzerackaityte, joe
[DESCRIPTION]
HiBit is an 11 amino acid protein tag that binds with high affinity to a larger subunit called LgBit. The bound complex has luciferase activity and will release luminescent signal in the presence of added furimazine substr... | ["[Protocol overview] Step 1: Design insert within Hibit construct, DNA synthesis\nStep 2: PCR amplify constructs\nStep 3: In vitro transcription-translation \nStep 4: Quantify protein RLU, normalize protein\nStep 5: First run an experiment for the positive control titrations and some other negative controls to determi... |
null | null | null | dx.doi.org/10.17504/protocols.io.r23d8gn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A real-time RT-PCR using an MGB probe, this assay detects Japanese encephalitis virus (JEV) from human and mosquito samples.</p>
<p>The assay targets the 3'UTR region of known JEV strains.</p>
[BEFORE_START]
<div>
<ul>
<li>If using a different brand or model of real-time the... | [] |
46,717 | Mitomycin C stem cell ablation | 4 | dx.doi.org/10.17504/protocols.io.bru5m6y6 | https://www.protocols.io/view/mitomycin-c-stem-cell-ablation-bru5m6y6 | Simon Blanchoud | TITLE: Mitomycin C stem cell ablation
AUTHORS: Simon Blanchoud
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Treatment is done for 24 h right after WBR 〈Whole Body Regeneration〉 induction. Tissue will not regenerate but haemolymph flow should be observable for around 20 days. A number of samples h... | ["[MMC solution]\nDissolve of MMC in of dH2O.\n1 mg\n500 µl", "[MMC solution]\nThis is the 1000x stock solution 〈 ).", "[MMC solution]\nAliquot this volume (we did it in ) and store at .\n100 µl\n-20 °C", "[MMC solution]\nMix of MMC stock solution with of FSW.\n10 µl\n990 µl", "[MMC solution]\nThis is the workin... |
48,233 | Ultrasensitive hybridization capture of short tuberculosis cell-free DNA from urine | 1 | null | https://www.protocols.io/view/ultrasensitive-hybridization-capture-of-short-tube-btchnit6 | Amy Oreskovic, Barry Lutz | TITLE: Ultrasensitive hybridization capture of short tuberculosis cell-free DNA from urine
AUTHORS: Amy Oreskovic, Barry Lutz
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Overview: This protocol describes a method for highly sensitive sequence-specific purificati... | ["[Urine collection and storage]\nBefore urine collection, prepare 15 mL Eppendorf DNA LoBind tubes with 500 μL 0.5 M EDTA and 100 μL 1M Tris-HCl pH 8.", "[Urine collection and storage]\nCollect urine sample in a sterile container.", "[Urine collection and storage]\nImmediately after urine collection, add 10 mL of urin... |
82,473 | How to 19F MRI: Supplemental protocol | 4 | dx.doi.org/10.17504/protocols.io.j8nlkw7kdl5r/v1 | https://www.protocols.io/view/how-to-19f-mri-supplemental-protocol-cushwwb6 | Olga Maxouri, z.elkarghali, Mariah Daal, Sajjad Rostami, Ivonne Rodriguez, Leila Akkari, Mangala Srinivas, Rene Bernards, Regina Beets-Tan | TITLE: How to 19F MRI: Supplemental protocol
AUTHORS: Olga Maxouri, z.elkarghali, Mariah Daal, Sajjad Rostami, Ivonne Rodriguez, Leila Akkari, Mangala Srinivas, Rene Bernards, Regina Beets-Tan
[DESCRIPTION]
This protocol is intended as a general guideline for in vivo 19F MRI experiments on a 7T Bruker system and Para... | ["[Preparation of the instruments] Check whether the desired RF coil (e.g. a dual-tuned 1H/19F birdcage coil) and animal cradle are connected to the MRI.", "[Preparation of the instruments] If inhalation anaesthetics are used, control the tubing towards the induction chamber and the animal cradle. Refill the isoflurane... |
57,760 | LABORATORY PROTOCOLS OF ANAEMIA TESTING USING PORTABLE HEMOCUE, MALARIA SCREENING USING RDT (HRP-2), PROCESSING OF WET PREPARATION, KATO-KATZ AND EXAMINATION OF STOOL SAMPLES, REPORTING OF SOIL-TRANSMITTED HELMINTHES AND FAECAL PARASITES (PREVALENCE AND | 4 | null | https://www.protocols.io/view/laboratory-protocols-of-anaemia-testing-using-port-b4m8qu9w | Jean Claude Nkurunziza, Aloys Niyongabo, Nicolette Nabukeera-Barungi, Joan Nakayaga Kalyango, Mercy Muwema Mwanja, Ezekiel Mupere, Joaniter I. Nankabirwa | TITLE: LABORATORY PROTOCOLS OF ANAEMIA TESTING USING PORTABLE HEMOCUE, MALARIA SCREENING USING RDT (HRP-2), PROCESSING OF WET PREPARATION, KATO-KATZ AND EXAMINATION OF STOOL SAMPLES, REPORTING OF SOIL-TRANSMITTED HELMINTHES AND FAECAL PARASITES (PREVALENCE AND
AUTHORS: Jean Claude Nkurunziza, Aloys Niyongabo, Nicol... | ["[MALARIA SCREENING USING RDT (HRP-2)] Open the alcohol swab and Clean the patient’s 4th finger towards the side of the pulp (if the subject is right-handed, choose the 4th finger on the left hand and vice-versa) or a heel prick in the case of children age 6-11 months, and allow it to air dry.", "[MALARIA SCREENING US... |
91,039 | Immuno Fluorescence staining of human FFPE (formalin fixed paraffin embedded) gut mucosal biopsy | 4 | dx.doi.org/10.17504/protocols.io.n2bvj3jrnlk5/v1 | https://www.protocols.io/view/immuno-fluorescence-staining-of-human-ffpe-formali-c457yy9n | Ran RZ Zhou | TITLE: Immuno Fluorescence staining of human FFPE (formalin fixed paraffin embedded) gut mucosal biopsy
AUTHORS: Ran RZ Zhou
[DESCRIPTION]
This protocol is to provide a detail instruction on the immuno fluorescence staining on human gut mucosal biopsy that has been preserved in FFPE and sectioned at 5 micron thickness... | ["[Deparaffinization] Immerse tissue sections on slides in Histoclear II in a staining dish Room temperature 5 min . Move the slide holder up and down x 5 times. Repeat this step two more times with fresh Histoclear II. There should be no visible paraffine remaining on the slide by the end of this step.", "[Rehydration... |
54,906 | DNA extraction from feathers | 4 | dx.doi.org/10.17504/protocols.io.bzu2p6ye | https://www.protocols.io/view/dna-extraction-from-feathers-bzu2p6ye | George Olah | TITLE: DNA extraction from feathers
AUTHORS: George Olah
[DESCRIPTION]
This protocol describes a DNA extraction method from feathers collected non-invasively in the wild.
[GUIDELINES]
Set up the extraction on a clean lab bench in a PCR-free area. Always use a negative control during each batch of extractions.
[STEP... | ["[Collection & Preparation] When collecting in the field, avoid touching the tip of the feathers. If wet, dry the feather on paper towel before storing it.\n\nPlace each feather sample in a separate paper envelope, labelling: individual sample ID, collection date, location, species, collector's name, etc.\n\nStore... |
37,022 | Find Proteins of Unknown Function (PUFs) using Plantannot - Protocol D | null | dx.doi.org/10.17504/protocols.io.bgd6js9e | https://www.protocols.io/view/find-proteins-of-unknown-function-pufs-using-plant-bgd6js9e | Marcos Viana, Adhemar Zerlotini, Mauricio Mudadu | TITLE: Find Proteins of Unknown Function (PUFs) using Plantannot - Protocol D
AUTHORS: Marcos Viana, Adhemar Zerlotini, Mauricio Mudadu
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The </span><span style = "font-style:italic;">Plantannot </span><span>software provides several filters and a... | ["[Entering application]\nEnter the Plantannot Result's page, with empty filters and text box search: https://www.machado.cnptia.embrapa.br/plantannot/find/?q=Or you can enter the https://www.machado.cnptia.embrapa.br/plantannot initial page and click on the magnifying glass with the text box empty as well.", "[Filte... |
72,293 | OpenVent Eco DNA Polymerase Production | 2 | null | https://www.protocols.io/view/openvent-eco-dna-polymerase-production-ciudues6 | Jenny Molloy, Stephane Fadanka, Nadine Mowoh | TITLE: OpenVent Eco DNA Polymerase Production
AUTHORS: Jenny Molloy, Stephane Fadanka, Nadine Mowoh
[DESCRIPTION]
This collection contains the protocols for production, quality control, packaging and use of Beneficial Bio's dehydrated OpenVent DNA Polymerase.
Format: 32 tubes (4x8-tube PCR strips) 20ul of... | [] |
45,379 | In vitro transcription of guide RNAs and 5'-triphosphate removal | 1 | dx.doi.org/10.17504/protocols.io.bqjbmuin | https://www.protocols.io/view/in-vitro-transcription-of-guide-rnas-and-5-triphos-bqjbmuin | Mark Dewitt, Julia Wong, Beeke Wienert, Moritz Schlapansky | TITLE: In vitro transcription of guide RNAs and 5'-triphosphate removal
AUTHORS: Mark Dewitt, Julia Wong, Beeke Wienert, Moritz Schlapansky
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">sgRNA template assembly, in vitro T7 transcription, and sgRNA column cleanup to remove 5'-triphosphate groups</... | ["[Design sgRNA and order PCR oligos.]\nAdd the desired protospacer sequence to the T7FwdVar oligo and order the oligo from your favorite oligonucleotide supplier. There are many programs available for protospacer design that attempt to optimize on- and/or off-target activity. Which program is most useful depends upon ... |
104,928 | Evercode Single Index PCR | 0 | dx.doi.org/10.17504/protocols.io.5jyl82k9rl2w/v1 | https://www.protocols.io/view/evercode-single-index-pcr-dip84drw | Parse Biosciences, Elisabeth Rebboah | TITLE: Evercode Single Index PCR
AUTHORS: Parse Biosciences, Elisabeth Rebboah
[DESCRIPTION]
This protocol describes the single-index PCR procedure for Parse Biosciences Evercode WT and WT Mega v2 kits. Each subpool is barcoded with a single Illumina index on the 3' end of the cDNA library. This acts as the fourth "ro... | ["[Appendix D2: Sublibrary Single Index PCR] If using unique dual indexes (UDIs) instead of sublibrary single index primers for indexing, see Section 3.5. Otherwise, replace the entirety of Section 3.5 with the following steps.\n\nMultiple thermocyclers may be needed for this section depending on the amount of cDNA add... |
59,800 | FLASH-seq protocol | 4 | dx.doi.org/10.17504/protocols.io.kxygxzkrwv8j/v3 | https://www.protocols.io/view/flash-seq-protocol-b6myrc7w | Simone Picelli, Vincent Hahaut | TITLE: FLASH-seq 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 over... | ["[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 mM0.240101.376SMART dT30VN (100 µM)1.8 mM0.0187.603RNAse inhibitor (40 U/µL)1.2 U/µL0.03012.672DTT (100 mM)1.2 mM0.0125.069FS TSO (100 µM)9.2 µM0.09... |
87,963 | Expression and Purification of SARS-CoV-2 Main Protease (Nonstructural Protein 5, NSP5) | 4 | dx.doi.org/10.17504/protocols.io.n2bvj391xlk5/v1 | https://www.protocols.io/view/expression-and-purification-of-sars-cov-2-main-pro-cz53x88n | Kaitlyn Varela, Francis K. Yoshimoto | TITLE: Expression and Purification of SARS-CoV-2 Main Protease (Nonstructural Protein 5, NSP5)
AUTHORS: Kaitlyn Varela, Francis K. Yoshimoto
[DESCRIPTION]
SARS-CoV-2 is the virus that caused the global COVID-19 pandemic in 2020-2023. This protocol describes how to express and purify the main protease of SARS-CoV-2 (n... | ["[A.1. Expression of Proteins in Bacteria I - Transformation (Day 1)] A.1. Transformation of Plasmid into Bacteria (Day 1)\n\nMaterials:\na. -78 ºC freezer\nb. ice in bucket\nc. Nitrile gloves\nd. Lab coat\ne. Safety glasses\nf. BL21 cells (Thermo Scientific Catalog number: EC0114)\ng. 2 mL microcentrifuge tube\nh. SO... |
96,813 | Adverse Outcomes of Combined Cochlear Implant and Hearing Aid Use: A Scoping Review | 0 | dx.doi.org/10.17504/protocols.io.dm6gp37xdvzp/v3 | https://www.protocols.io/view/adverse-outcomes-of-combined-cochlear-implant-and-dasm2ec6 | augustina.noel, Priyanka Jaisinghani | TITLE: Adverse Outcomes of Combined Cochlear Implant and Hearing Aid Use: A Scoping Review
AUTHORS: augustina.noel, Priyanka Jaisinghani
[DESCRIPTION]
Relevant articles highlighting adverse outcomes with the combination of hearing aid and cochlear implant published between 2000 and 2023 will be searched using manual s... | ["[Review Demographic details] Title: Adverse Outcomes of Combined Cochlear Implant and Hearing Aid Use: A Scoping Review.", "[Review Demographic details] Original language title: English", "[Review Demographic details] Start Date: 25/02/2024", "[Review Demographic details] End Date: 25/02/25", "[Review Demographic det... |
69,022 | Preparation and imaging of enriched Golgi from GolgiTAG-IP using Transmission Electron Microscopy | 1 | dx.doi.org/10.17504/protocols.io.x54v9y9nqg3e/v1 | https://www.protocols.io/view/preparation-and-imaging-of-enriched-golgi-from-gol-cfm6tk9e | Rotimi Fasimoye, Alan Prescott, Dario R Alessi | TITLE: Preparation and imaging of enriched Golgi from GolgiTAG-IP using Transmission Electron Microscopy
AUTHORS: Rotimi Fasimoye, Alan Prescott, Dario R Alessi
[DESCRIPTION]
Transmission electron microscopy (TEM) is a tool used to image, in good resolution, the structure of organelles within the cell. Available proto... | ["[Method] Perform GolgiTAG-IP as previously described in dx.doi.org/10.17504/protocols.io.6qpvrdjrogmk/v1", "[Method] After last wash of beads with KPBS, fix the beads in 1 mL solution containing 4% (w/v) paraformaldehyde and 2.5% (v/v) glutaraldehyde in 0.1 Molarity (M) sodium cacodylate buffer dilute in water for 60... |
68,526 | Agarose Gel Electrophoresis (Instructor Protocol) | 4 | null | https://www.protocols.io/view/agarose-gel-electrophoresis-instructor-protocol-ce6nthde | Brian Teague | TITLE: Agarose Gel Electrophoresis (Instructor Protocol)
AUTHORS: Brian Teague
[DESCRIPTION]
This is the instructor protocol for
The protocol is pretty straightforward, but I have included several common student errors to watch out for!
[STEPS]
SECTION: Make the LAB buffer
1. Make LAB buffer following this reci... | ["[Make the LAB buffer] Make LAB buffer following this recipe:\n \n\nFor a class of 24, I usually prepare 6x 1 L bottles of 1X LAB. We go through a lot -- there are three gels that get run over the course of the semester, plus repeats.", "[Instructor Tips & Common Student Errors] Instructor Tips\nThe benefit of usi... |
47,094 | Converting microscopy image data and metadata with Microfile+: 2D images into a 3D stack | 1 | null | https://www.protocols.io/view/converting-microscopy-image-data-and-metadata-with-br8wm9xe | Maci Heal | TITLE: Converting microscopy image data and metadata with Microfile+: 2D images into a 3D stack
AUTHORS: Maci Heal
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Enrich the metadata and FAIRness of microscopy image data by converting into OME-TIFF and/or JPEG2000 format with Microfile+. </div></div... | ["MicroFile+ is a free tool compatible with Windows workstations. Download and install Microfile+ by going to https://www.mbfbioscience.com/microfileplus. Once installed, launch the MicroFile+ application.", "Select Combine 2D images into a 3D stack\nImages can be converted from image to image, series to image, many ch... |
5,176 | Preparation and Transformation of Competent E. coli cells (CCMB80 Method) | null | dx.doi.org/10.17504/protocols.io.hayb2fw | null | Tobias von der Haar | TITLE: Preparation and Transformation of Competent E. coli cells (CCMB80 Method)
AUTHORS: Tobias von der Haar
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This method is based on that originally described by </span><a href="https://www.ncbi.nlm.nih.gov/pubmed/1943786" style = "text-decorati... | ["[Preparation of Bacterial Seed Stocks]\nPick single colonies from the stock plate into 5 ml of SOB or LB medium and shake overnight at 30°C.\n Add 600 μl of glycerol (15% final concentration) to the culture\n Aliquot 1 ml samples into cryotubes and place in a -80ºC freezer for long-term storage.", "[Preparation of Gl... |
95,883 | ddPCR for probes to target eDNA samples : from sample preparation to droplet reading | 4 | dx.doi.org/10.17504/protocols.io.n92ldm479l5b/v1 | https://www.protocols.io/view/ddpcr-for-probes-to-target-edna-samples-from-sampl-c9vjz64n | Marine Vautier, Cecile Chardon, Cyrielle Galiegue, Isabelle Domaizon | TITLE: ddPCR for probes to target eDNA samples : from sample preparation to droplet reading
AUTHORS: Marine Vautier, Cecile Chardon, Cyrielle Galiegue, Isabelle Domaizon
[DESCRIPTION]
The aim of this protocol is the digital droplet PCR (ddPCR) quantification of DNA target(s) using primer and probe sets. This protocol ... | ["[Material preparation] Pre and post extraction equipment decontamination:\n- Specific DNA-workstation: UV decontamination.\n\nTurn on the following equipments: \n- the QX200 droplet generator \n- the PX1 PCR plate sealer at 180 °C\n- the thermal cycler for PCR\n- the QX600 or QX200 droplet reader for ddPCR\n\nTubes a... |
null | null | null | dx.doi.org/10.17504/protocols.io.qsjdwcn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?. | [] |
53,948 | UW Virology Swift SNAPv2 protocol | 1 | null | https://www.protocols.io/view/uw-virology-swift-snapv2-protocol-byw4pxgw | Lasata Shrestha, Hong Xie, Shah A. Mohamed Bakhash, Robert J. Livingston, Meei-Li Huang, Alexander L. Greninger, Pavitra Roychoudhury | TITLE: UW Virology Swift SNAPv2 protocol
AUTHORS: Lasata Shrestha, Hong Xie, Shah A. Mohamed Bakhash, Robert J. Livingston, Meei-Li Huang, Alexander L. Greninger, Pavitra Roychoudhury
[DESCRIPTION]
Viral whole genome sequencing (WGS) has been instrumental in outbreak investigations, deployment of public health interve... | ["[Sciclone Movements: Swift SNAP v2 Multiplex PCR]", "[Sciclone Movements: Swift SNAP v2 Multiplex PCR] Pipette multiplex master-mix ( A4 to samples on D4)", "[Sciclone Movements: Swift SNAP v2 Multiplex PCR] Dispose off tips", "[Sciclone Movements: Swift SNAP v2 Multiplex PCR] Lid from A2 to A4", "[Sciclone Movements... |
27,755 | Prepare Uric Acid Solution | null | dx.doi.org/10.17504/protocols.io.7cjhiun | null | 宏亮 董 | TITLE: Prepare Uric Acid Solution
AUTHORS: 宏亮 董
[STEPS]
?. Prepare Uric Acid Storage Solution:Accurately weigh 0.01g uric acid dissolved in Uric Acid Diluent Solution and dilute to 100mL;
?. Prepare Borate Buffer Storage Solution:Add these reagents to a clean media bottle, DDW volume to 200ml, adjust pH to 8.5 with Na... | ["Prepare Uric Acid Storage Solution:Accurately weigh 0.01g uric acid dissolved in Uric Acid Diluent Solution and dilute to 100mL;", "Prepare Borate Buffer Storage Solution:Add these reagents to a clean media bottle, DDW volume to 200ml, adjust pH to 8.5 with NaOH. AB1boric acid6.185g2borax9.535g3EDTA1.169g410% Triton... |
85,642 | KAPP-Sen TMC: Preparation of Workspace for Tissue Blocks Sectioning | 1 | dx.doi.org/10.17504/protocols.io.36wgq37polk5/v1 | https://www.protocols.io/view/kapp-sen-tmc-preparation-of-workspace-for-tissue-b-cxvixn4e | Juliana Alcoforado Diniz, Elaine Bechtel, Paul Robson | TITLE: KAPP-Sen TMC: Preparation of Workspace for Tissue Blocks Sectioning
AUTHORS: Juliana Alcoforado Diniz, Elaine Bechtel, Paul Robson
[DESCRIPTION]
Preparation of Workspace for Tissue Blocks Sectioning
[STEPS]
SECTION: Preparation of Workspace
1. Wear nitrile gloves cleaned with RNase Zap wipe.
SECTION: Preparat... | ["[Preparation of Workspace] Wear nitrile gloves cleaned with RNase Zap wipe.", "[Preparation of Workspace] Using RNase Zap wipes, clean microtome including any surface block or hands may contact (block holder, knife holder, handle, etc.).", "[Preparation of Workspace] Using RNase Zap wipes, clean glass Pyrex water bat... |
27,743 | Algal nuclei isolation for Nanopore sequencing of HMW DNA | null | dx.doi.org/10.17504/protocols.io.7b7hirn | null | Robert Auber, Jennifer Wisecaver | TITLE: Algal nuclei isolation for Nanopore sequencing of HMW DNA
AUTHORS: Robert Auber, Jennifer Wisecaver
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol was developed for extraction of high molecular weight (HMW) DNA from </span><span style = "font-style:italic;">Prymnesium par... | ["[Prepare equipment and reagents]\nChill centrifuge to\n4 °C", "[Prepare equipment and reagents]\nChill 50 ml conical tubes (4 per sample) and NIB buffers on ice.", "[Cell Lysis]\nTransfer to of culture to a pre-chilled 50 ml conical tube and centrifuge at for to pellet cells.The amount of culture spun down as... |
null | null | null | dx.doi.org/10.17504/protocols.io.mn8c5hw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?. | [] |
55,047 | Risk perception and coping response to COVID-19 is mediated by positive and negative emotions: a study on Chinese college students | 3 | null | https://www.protocols.io/view/risk-perception-and-coping-response-to-covid-19-is-bzzfp73n | ganyt | TITLE: Risk perception and coping response to COVID-19 is mediated by positive and negative emotions: a study on Chinese college students
AUTHORS: ganyt
[DESCRIPTION]
This study aimed to assess the mediating roles of positive and negative emotions on the relationship between COVID-19-related risk perception and copi... | [] |
70,981 | Nuclei Extraction for tissue using Iodixanol Gradients | 1 | dx.doi.org/10.17504/protocols.io.81wgby7yqvpk/v1 | https://www.protocols.io/view/nuclei-extraction-for-tissue-using-iodixanol-gradi-chjdt4i6 | Kriegstein lab | TITLE: Nuclei Extraction for tissue using Iodixanol Gradients
AUTHORS: Kriegstein lab
[DESCRIPTION]
Nuclei isolation using Iodixanol gradients geared for multiome
[STEPS]
SECTION: Creating Buffers
1. Stock Buffers
All stock solutions should be filtered using a .22 um PVDF/PES filter system. All solutions except 50% I... | ["[Creating Buffers] Stock Buffers\nAll stock solutions should be filtered using a .22 um PVDF/PES filter system. All solutions except 50% Iodixanol solution are stable at 4c for at least 6 months.\n\n1 M Sucrose (300 mL)\nSubstance: Stock Conc.: Amount: Final conc. in working s... |
93,111 | Free floating Immunofluorescence protocol for mouse brain sections | 4 | dx.doi.org/10.17504/protocols.io.n92ldm1nnl5b/v2 | https://www.protocols.io/view/free-floating-immunofluorescence-protocol-for-mous-c66xzhfn | Felicia Xaveria Suteja, YuHong Fu, Tony Hsiao | TITLE: Free floating Immunofluorescence protocol for mouse brain sections
AUTHORS: Felicia Xaveria Suteja, YuHong Fu, Tony Hsiao
[DESCRIPTION]
Free floating Immunofluorescence protocol with multiplexing labelling for mouse brain sections
[STEPS]
SECTION: Day 1
2. Remove samples from freezer and equilibrate at room te... | ["[Day 1] Remove samples from freezer and equilibrate at room temperature (RT) for 10 - 20 minutes.", "[Day 1] Pour sections into a well insert in a 6-well plate with 1X PBS to separate storage solution from sections. Change 1X PBS before step 3.", "[Day 1] Wash once with 1X PBS for 20 minutes and once with 1X PBS for ... |
90,560 | Sleep-Wake Recording in the Turek Laboratory | 1 | dx.doi.org/10.17504/protocols.io.yxmvm3z29l3p/v1 | https://www.protocols.io/view/sleep-wake-recording-in-the-turek-laboratory-c4n8yvhw | Keith C Summa | TITLE: Sleep-Wake Recording in the Turek Laboratory
AUTHORS: Keith C Summa
[DESCRIPTION]
Surgery and recording protocol for measuring sleep-wake behavior in mice
[STEPS]
SECTION: Surgery
1. The mouse is anesthetized by intraperitoneal injection with a ketamine/xylazine cocktail. Once the animal is anesthetized (as... | ["[Surgery] The mouse is anesthetized by intraperitoneal injection with a ketamine/xylazine cocktail. Once the animal is anesthetized (as assessed by toe pinch), the fur on the top of the head is wetted with diluted alcohol and clipped.", "[Surgery] The animal is positioned in the stereotaxis apparatus (David Kopf Inst... |
104,248 | Treatment of D. melanogaster with small molecules in fly food | 0 | dx.doi.org/10.17504/protocols.io.bp2l62rozgqe/v1 | https://www.protocols.io/view/treatment-of-d-melanogaster-with-small-molecules-i-dh2y38fw | Natalie Kaempf, Patrik Verstreken | TITLE: Treatment of D. melanogaster with small molecules in fly food
AUTHORS: Natalie Kaempf, Patrik Verstreken
[DESCRIPTION]
This protocol describes the preparation of fly food with small molecules to treat flies during their aging. It can be adapted for any treatments. Details for small molecules used can be found i... | ["[Food preparation] warm up the amount of fly food (standard corn meal and molasses food) required (e.g. 50ml for 45 XS vials) in the microwave, stir it in between, start with 1.5 min, mix the food, heat up for 1min again and continue until food has no clumbs anymore", "[Food preparation] prepare XS vials (45 for each... |
null | null | null | dx.doi.org/10.17504/protocols.io.kzxcx7n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The present protocol explains how to prepare a primary culture of isolated neurons from the mouse nodose ganglion.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
86,197 | Viral infection | 4 | null | https://www.protocols.io/view/viral-infection-cyevxte6 | Louise Uoselis | TITLE: Viral infection
AUTHORS: Louise Uoselis
[DESCRIPTION]
Protocol for generation and precipitation of retrovirus and infection of LHeLa cells
[STEPS]
SECTION: Day 1
1. Seed HEK293T cells into a 10cm tissue culture plate (6.1 million cells/plate), seeding one plate per construct you are generating virus for.
SEC... | ["[Day 1] Seed HEK293T cells into a 10cm tissue culture plate (6.1 million cells/plate), seeding one plate per construct you are generating virus for.", "[Day 2] Transfect cells with viral and helper vectors using lipofectamine LTX. In a 15mL falcon tube, combine the following:\n \n Reagent Amount ... |
null | null | null | dx.doi.org/10.17504/protocols.io.e2vbge6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Target cells are depleted by incubating your sample with the biotin antibody cocktail followed by incubation with magnetic Streptavidin Nanobeads (Cat. No. 480015/480016). The magnetically labeled fraction is retained by the use of a magnetic separator. The untouched cells ar... | [] |
54,645 | Comparative efficacy of sedation or analgesia methods for reduction of anterior shoulder dislocation: a systematic review and network meta-analysis | 1 | dx.doi.org/10.17504/protocols.io.bzkvp4w6 | https://www.protocols.io/view/comparative-efficacy-of-sedation-or-analgesia-meth-bzkvp4w6 | Minoru Hayashi, Kenichi Kano, Naoto Kuroda, Norio Yamamoto, Akihiro Shiroshita, Yuki Kataoka | TITLE: Comparative efficacy of sedation or analgesia methods for reduction of anterior shoulder dislocation: a systematic review and network meta-analysis
AUTHORS: Minoru Hayashi, Kenichi Kano, Naoto Kuroda, Norio Yamamoto, Akihiro Shiroshita, Yuki Kataoka
[DESCRIPTION]
The objectives are as follows:
To review system... | [] |
91,123 | SW-5 SWAB SHIPPING | 4 | dx.doi.org/10.17504/protocols.io.eq2lyj2nrlx9/v1 | https://www.protocols.io/view/sw-5-swab-shipping-c48tyzwn | REDI-NET Consortium | TITLE: SW-5 SWAB SHIPPING
AUTHORS: REDI-NET Consortium
[DESCRIPTION]
This protocol describes swab shipping.
[GUIDELINES]
OBJECTIVE
To outline steps for proper packaging and shipping of preserved swab samples from a REDI-NET Silver Lab to a REDI-NET Gold Lab.
SUMMARY/SCOPE
The overarching aim of the REDI-NET is to ... | ["[SAMPLE PREPARATION] Primary holding sample holding containers must be leak-proof. Samples should be preserved in appropriate preservative, if applicable (REDI-NET Swab Processing SOP SW-2). Ensure that the lids are tightly closed to prevent leaking of storage media while in transit.", "[SAMPLE PREPARATION] Pack vial... |
37,133 | Preliminary Evaluation of RNA Extraction Methods | 1 | null | https://www.protocols.io/view/preliminary-evaluation-of-rna-extraction-methods-bghmjt46 | Aniela Wozniak, Catalina Ibarra-Henriquez, Valentina Sebastian, Grace Armijo, Liliana Lamig, Carolina Miranda, Marcela Lagos, Sandra Solari, Ana María Guzmán, Teresa Quiroga, Susan Hitschfeld, Eleodoro Riveras, Marcela Ferres, Rodrigo A. Gutiérrez, Patricia García, Ariel Cerda | TITLE: Preliminary Evaluation of RNA Extraction Methods
AUTHORS: Aniela Wozniak, Catalina Ibarra-Henriquez, Valentina Sebastian, Grace Armijo, Liliana Lamig, Carolina Miranda, Marcela Lagos, Sandra Solari, Ana María Guzmán, Teresa Quiroga, Susan Hitschfeld, Eleodoro Riveras, Marcela Ferres, Rodrigo A. Gutiérrez, Patric... | ["[Biological Samples]\nObtain two saliva samples from each asymptomatic volunteer and perform at least three independent RNA extractions from each sample, obtaining a minimum of six RNA preparations to test each experimental procedure.\nTwo types of biological samples were used:For preliminary evaluation of the RNA ex... |
null | null | null | dx.doi.org/10.17504/protocols.io.cpmvk5 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?. | [] |
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