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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81,461 | 10x Protocols: Visium v2 CytAssist FFPE Deparaffinization, H&E staining, and Imaging-- University of Minnesota TMCs (CG000520 Rev B) | 1 | dx.doi.org/10.17504/protocols.io.dm6gpjpyjgzp/v1 | https://www.protocols.io/view/10x-protocols-visium-v2-cytassist-ffpe-deparaffini-ctsvwne6 | IOx Genomics, Laura J Niedernhofer, David A Bernlohr | TITLE: 10x Protocols: Visium v2 CytAssist FFPE Deparaffinization, H&E staining, and Imaging-- University of Minnesota TMCs (CG000520 Rev B)
AUTHORS: IOx Genomics, Laura J Niedernhofer, David A Bernlohr
[DESCRIPTION]
Protocols from 10x Genomics for Visium Spatial Gene Expression v2 chemistry on FPPE samples with th... | ["10x protocol CG000520, Revision B (Deparaffinization, H&E staining and Imaging prior to Library Construction and CytAssist)", "Additional Protocols/Resources\nhttps://www.10xgenomics.com/support/spatial-gene-expression-ffpe"] |
78,214 | Viral purification from bacterial culture | 4 | dx.doi.org/10.17504/protocols.io.e6nvwjq7wlmk/v1 | https://www.protocols.io/view/viral-purification-from-bacterial-culture-cqmevu3e | sarah.schulz | TITLE: Viral purification from bacterial culture
AUTHORS: sarah.schulz
[DESCRIPTION]
Protocol for the purification of viral particles from bacterial liquid culture
[STEPS]
1. Centrifuge 40 ml of bacterial culture infected with phage at 6000 g for 30 min, remove the supernatant and filter it through a 0.45 μm syringe ... | ["Centrifuge 40 ml of bacterial culture infected with phage at 6000 g for 30 min, remove the supernatant and filter it through a 0.45 μm syringe filter", "Centrifuge the filtrate at 35 000 g for 4 h, remove the supernatant and re-suspend the pellet in 600 μl SM buffer", "Add 2 μl of DNAse I and 20 μl of 10x DNAse buffe... |
59,507 | Unclear insomnia types in randomized controlled trials and systematic reviews: the protocol for a meta-epidemiological study | 1 | dx.doi.org/10.17504/protocols.io.kxygxz3bkv8j/v2 | https://www.protocols.io/view/unclear-insomnia-types-in-randomized-controlled-tr-b6ctrawn | Masahiro Banno, Yasushi Tsujimoto, Kunihiro Kohmura, Eisuke Dohi, Shunsuke Taito, Hidehiro Someko, Yuki Kataoka | TITLE: Unclear insomnia types in randomized controlled trials and systematic reviews: the protocol for a meta-epidemiological study
AUTHORS: Masahiro Banno, Yasushi Tsujimoto, Kunihiro Kohmura, Eisuke Dohi, Shunsuke Taito, Hidehiro Someko, Yuki Kataoka
[DESCRIPTION]
Objectives. To examine tendencies and charac... | ["[BACKGROUND] Insomnia disorder is diagnosed when both nocturnal insomnia symptoms and daytime dysfunctions continued for at least 1 month in the tenth revision of the International Statistical Classification of Diseases and Related Health Problems (ICD-10), and for at least 3 months in the third edition of the Intern... |
90,947 | Environmental DNA (eDNA) 12S Metabarcoding Illumina MiSeq NGS Protocol with size selection | 1 | null | https://www.protocols.io/view/environmental-dna-edna-12s-metabarcoding-illumina-c43byyin | Kathleen Pitz, jbaker | TITLE: Environmental DNA (eDNA) 12S Metabarcoding Illumina MiSeq NGS Protocol with size selection
AUTHORS: Kathleen Pitz, jbaker
[DESCRIPTION]
This sequencing protocol is intended to directly follow and use the PCR products of the protocol:
"Environmental DNA (eDNA) 12S Metabarcoding PCR Protocol (with Platinum SuperF... | ["[MIOP: Minimum Information about an Omics Protocol] MIOP Term\nValue\n \nmethodology category\n\n \nproject\n\n \npurpose\n\n \nanalyses\n\n \ngeographic location\n\n \nbroad-scale environmental context\n\n \nlocal environmental context\n\n \nenvironmental medium\n\n \ntarget\n\n \ncreator\n\n \nmaterials required\... |
81,948 | Complete Medium or Complete Medium Xylose (from Leach, Lang and Yoder 1982) | 4 | dx.doi.org/10.17504/protocols.io.kqdg39mxqg25/v2 | https://www.protocols.io/view/complete-medium-or-complete-medium-xylose-from-lea-ct94wr8w | Megan Mcdonald | TITLE: Complete Medium or Complete Medium Xylose (from Leach, Lang and Yoder 1982)
AUTHORS: Megan Mcdonald
[DESCRIPTION]
For the growth and maintenance of Cochliobolus carbonum and Cochliobolus victoriae
[STEPS]
SECTION: Make Micronutrients Solution
1. 9 mg H3BO3
58.5 mg CuSO4 *5H2O
1.95 mg KI (Potassium Iodine)
9 ... | ["[Make Micronutrients Solution] 9 mg H3BO3\n58.5 mg CuSO4 *5H2O\n1.95 mg KI (Potassium Iodine)\n9 mg MnSO4\n7.6 mg NaMoO4\n822 mg ZnSO4 * 6 H2O\n139.8 mg FeCl3 * 6H2O\n\nin 300 mL ddH2O and filter sterilise\n\nCitation:\nHeterokaryosis and Parasexuality in the Fungus Ascochyta Imperfecta Author(s): K. E. Sanderson an... |
39,929 | Nextera Flex DNA | 3 | dx.doi.org/10.17504/protocols.io.bi8zkhx6 | https://www.protocols.io/view/nextera-flex-dna-bi8zkhx6 | John E Gorzynski | TITLE: Nextera Flex DNA
AUTHORS: John E Gorzynski
[STEPS] | [] |
98,726 | DENV2 NS2B-NS3 protease co-expression construct small scale expression and purification protocol | 1 | dx.doi.org/10.17504/protocols.io.rm7vzj362lx1/v1 | https://www.protocols.io/view/denv2-ns2b-ns3-protease-co-expression-construct-sm-dcne2vbe | Korvus Wang, michael fairhead, Eleanor Williams | TITLE: DENV2 NS2B-NS3 protease co-expression construct small scale expression and purification protocol
AUTHORS: Korvus Wang, michael fairhead, Eleanor Williams
[DESCRIPTION]
This protocol details the co-expression and purification of DENV2 NS2B-NS3 protease construct bearing a N-terminal His-GST tag at small scale (<... | ["[Plasmid Transformation] DVNS2B3 N-terminal His-GST tagged co-expression construct was inoculated from its BL21(DE3)-RR glycerol stock.", "[Protein expression] When the OD600 approximately 1.8, add 1mM IPTG. Lower the temperature and shaker speed to . Incubate overnight.", "[Protein Purifcation] Perform IMAC to extr... |
55,599 | RNA Extraction Protocol for Shorea | 4 | dx.doi.org/10.17504/protocols.io.b2ipqcdn | https://www.protocols.io/view/rna-extraction-protocol-for-shorea-b2ipqcdn | mpfsum | TITLE: RNA Extraction Protocol for Shorea
AUTHORS: mpfsum
[DESCRIPTION]
RNA extraction protocol using CTAB method optimized for leaf and bud samples from Shorea curtisii.
Adapted from extraction protocol for Shorea beccariana (see attached publication).
[STEPS]
SECTION: Lysis
1. Weigh BUD 40 mg or LEAF 60 mg and tr... | ["[Lysis] Weigh BUD 40 mg or LEAF 60 mg and transfer into a 1.5 mL tube.", "[Lysis] Ground in CTAB buffer (3% CTAB, 1.4 M NaCl, 20 mM EDTA, 100 mM Tris–HCl pH 8.0, 0.2% b-mercaptoethanol) using tissuelyzer.", "[Lysis] Incubate at 60 °C for 45 min.", "[Precipitation] Add 1 volume of chloroform.\nMix by vortex but not to... |
19,902 | Lake plankton sample collection from the field for downstream molecular analysis | null | dx.doi.org/10.17504/protocols.io.xn6fmhe | null | Isabelle Domaizon, Rainer Kurmayer, Camilla Capelli, Cécile Chardon, Peter Hufnagl, Marine Vautier, Nico Salmaso | TITLE: Lake plankton sample collection from the field for downstream molecular analysis
AUTHORS: Isabelle Domaizon, Rainer Kurmayer, Camilla Capelli, Cécile Chardon, Peter Hufnagl, Marine Vautier, Nico Salmaso
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align... | ["[SCIENTIFIC CONTEXT & GENERAL DESCRIPTION OF SAMPLING]\nPhytoplankton (including cyanobacteria) is routinely used to define the ecological quality status of lakes. The traditional method to produce metrics/indices from phytoplankton is based on the direct observation of the organisms (morphological identification of ... |
108,568 | Treatment schemes and persistence in Colombian patients diagnosed with inflammatory arthritis after the failure of conventional disease-modifying antirheumatic drugs | 0 | dx.doi.org/10.17504/protocols.io.kqdg32z31v25/v1 | https://www.protocols.io/view/treatment-schemes-and-persistence-in-colombian-pat-dm9y497w | Jorge Machado Alba | TITLE: Treatment schemes and persistence in Colombian patients diagnosed with inflammatory arthritis after the failure of conventional disease-modifying antirheumatic drugs
AUTHORS: Jorge Machado Alba
[DESCRIPTION]
Introduction:
Inflammatory arthritis is related to disability, chronic pain, and premature
death. A lack... | [] |
83,097 | Glia-Free Cortical Neuronal Feeding Schedule - Synapse Formation | 4 | dx.doi.org/10.17504/protocols.io.j8nlkobodv5r/v1 | https://www.protocols.click/view/glia-free-cortical-neuronal-feeding-schedule-synap-cvdzw276 | Justin T Savage, Juan Ramirez, Dolores Irala, Cagla Eroglu | TITLE: Glia-Free Cortical Neuronal Feeding Schedule - Synapse Formation
AUTHORS: Justin T Savage, Juan Ramirez, Dolores Irala, Cagla Eroglu
[DESCRIPTION]
Protocol for isolating rat cortical astrocytes and producing astrocyte-conditioned media for synaptogenesis assays.
[STEPS]
SECTION: Neuronal growth media (NGM) for... | ["[Neuronal growth media (NGM) for feeding] This recipe makes 20ml of neuronal media. Make fresh per use", "[Neuronal growth media (NGM) for feeding] To a 50ml tube, add the following media components:\n \n Reagent Volume Neurobasal plus 19ml Pen/strep (100x) 200µl ... |
69,433 | Integra Total Nucleic Acid Extraction | 1 | dx.doi.org/10.17504/protocols.io.81wgbydq1vpk/v1 | https://www.protocols.io/view/integra-total-nucleic-acid-extraction-cf2ztqf6 | Sophana Chea, Sreyngim Lay, Mengheng Oum, Gechlang Tang, Cheata Hou, Manu Vanaerschot, Christina Yek, Jessica Manning, Vida Ahyong | TITLE: Integra Total Nucleic Acid Extraction
AUTHORS: Sophana Chea, Sreyngim Lay, Mengheng Oum, Gechlang Tang, Cheata Hou, Manu Vanaerschot, Christina Yek, Jessica Manning, Vida Ahyong
[DESCRIPTION]
This SOP is the process of extracting Total Nucleic Acid (TNA) from Sera and/or Nasopharyngeal or Nasal swabs. The isola... | ["[Reagent preparation (required with new kit)] 1. Add 20 mL of isopropanol to the MagBead DNA/RNA Wash 1 concentrate.\n2. Add 30 mL of isopropanol to the MagBead DNA/RNA Wash 2 concentrate.\n3. Add 1.2 mL of Proteinase K Storage Buffer per vial to reconstitute the lyophilized Proteinase K at 20 mg/mL \nVortex to disso... |
55,858 | Intracardiac perfusion with fixative for ultrastructural neuroanatomical studies | 1 | dx.doi.org/10.17504/protocols.io.b2ssqeee | https://www.protocols.io/view/intracardiac-perfusion-with-fixative-for-ultrastru-b2ssqeee | Janet R Keast, Peregrine Osborne | TITLE: Intracardiac perfusion with fixative for ultrastructural neuroanatomical studies
AUTHORS: Janet R Keast, Peregrine Osborne
[DESCRIPTION]
This protocol is suitable for preserving tissues for ultrastructural neuroanatomical studies of peripheral nerves, ganglia, spinal cord or brain in adult rats. The protocol is... | ["[Perfusion] Induce anesthesia by an intraperitoneal injection of ketamine (100 mg/kg) and xylazine (10 mg/kg).", "[Perfusion] After opening the chest cavity, inject the left ventricle with mixture of 0.25 ml heparin (5000 IU/ml) and 0.5 ml 1% sodium nitrite.", "[Perfusion] A needle connected to tubing (T-connector to... |
15,173 | JM SW modified medium | null | dx.doi.org/10.17504/protocols.io.s3degi6 | null | Roscoff Culture Collection | TITLE: JM SW modified medium
AUTHORS: Roscoff Culture Collection
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Medium used for Cryptophytes</div><div class = "text-block">Adapted from CCAP web site: http://www.ife.ac.uk/ccap/MediaRecipes2.html#jm </div></div>
[STEPS]
?. Change from standard JM ... | ["Change from standard JM medium ABCDE1Volume for 1 litre\nComponent\nConcentration Stock Solutions\n21 ml\nKH2PO4\nKH2PO4\n2.48 gr\n200 ml\n31 ml\nCaCl2\nCaCl2.2H2O\n0.5 gr\n200 ml\n42 ml\nNaNO3\nNaNO3\n16 gr\n200 ml\n51 ml\nMgSO4\nMgSO4.7H2O\n10 gr\n200 ml\n61 ml\nNaHCO3\nNaHCO3\n3.18 gr\n200 ml\n71 ml\nNa2EDTA.FeCl... |
49,646 | SARS-CoV-2 ENA submission workflow + guidance for structuring and releasing metadata | 2 | dx.doi.org/10.17504/protocols.io.buqnnvve | https://www.protocols.io/view/sars-cov-2-ena-submission-workflow-guidance-for-st-buqnnvve | Nabil-Fareed Alikhan, Ruth E Timme, Emma Griffiths, Emma Griffiths | TITLE: SARS-CoV-2 ENA submission workflow + guidance for structuring and releasing metadata
AUTHORS: Nabil-Fareed Alikhan, Ruth E Timme, Emma Griffiths, Emma Griffiths
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">PURPOSE:</span></div><div class = "text-block"><sp... | [] |
101,151 | MUSIC Protocol | 1 | dx.doi.org/10.17504/protocols.io.4r3l22kwxl1y/v2 | https://www.protocols.io/view/music-protocol-dez73f9n | Wenxin Zhao, Zhifei Luo, Sheng Zhong | TITLE: MUSIC Protocol
AUTHORS: Wenxin Zhao, Zhifei Luo, Sheng Zhong
[DESCRIPTION]
Here we introduce the Multi-Nucleic Acid Interaction Mapping in Single Cell (MUSIC) technique for concurrent profiling of multiplex chromatin interactions, gene expression, and RNA-chromatin associations within individual nuclei. MUSIC p... | ["[Crosslinking and nuclei isolation for cell lines] Wash cell culture with ice-cold PBS.", "[5' Phosphorylation] Resuspend nuclei in 250 µL of 5’ phosphorylation master mix followed by an incubation at 37°C while rotating at 800 rpm for 1 hour.", "[Ligation of cell barcodes] Anneal cell barcodes.", "[Ligation of ... |
80,784 | 2-step PCR mixture and conditions (Barcoded-head primers for seqs pooling) | 4 | dx.doi.org/10.17504/protocols.io.yxmvm263og3p/v1 | https://www.protocols.io/view/2-step-pcr-mixture-and-conditions-barcoded-head-pr-cs5qwg5w | Yin-Tse Huang, Tsu-Chun Hung | TITLE: 2-step PCR mixture and conditions (Barcoded-head primers for seqs pooling)
AUTHORS: Yin-Tse Huang, Tsu-Chun Hung
[DESCRIPTION]
PCR mixture and condition (2X SUPERGREEN PCR MASTER MIX)
[STEPS]
1. Wear glove, clean up the working bench w. 1% bleach
SECTION: For 1' PCR head-primers
2. Prepare 1' PCR master... | ["Wear glove, clean up the working bench w. 1% bleach", "[For 1' PCR head-primers] Prepare 1' PCR master mixutre for head-primers (prepare 1.2X of solutions for pipetting error if needed)\n \nPCR mixture for head-primers for each reaction", "[For 1' PCR head-primers] Mix the 1' PCR master mixture gently by pi... |
31,982 | Case Processing SOP for Lymph Nodes | null | dx.doi.org/10.17504/protocols.io.bbgnijve | null | Marda Jorgensen, Jerelyn Nick | TITLE: Case Processing SOP for Lymph Nodes
AUTHORS: Marda Jorgensen, Jerelyn Nick
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The purpose of this Standard Operating Procedure is to outline procedures for processing and storing lymph node tissue received for HuBMAP consortium assay and analysis.... | ["The tissues received will be identified as follows: Lymph Node (LN)", "Sample prepared from tissues will be identified using the following nomenclature, abbreviations, and formats: Formalin Fixed Paraffin Embedded---FFPE (paraffin block)Formalin Fixed Frozen Embedded---Fixed OCT BlockFresh Frozen Embedded---Fresh OCT... |
35,365 | Patch-Seq Internal Solution with Biocytin | null | dx.doi.org/10.17504/protocols.io.besdjea6 | null | Allen Institute for Brain Science | TITLE: Patch-Seq Internal Solution with Biocytin
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This SOP provides instruction to prepare Internal Solution which is used for patch clamp electrophysiology, modified for cleanliness and mRNA capture and sustai... | [] |
80,323 | NCBI submission protocol for microbial pathogen surveillance | 1 | dx.doi.org/10.17504/protocols.io.4r3l284pql1y/v8 | https://www.protocols.io/view/ncbi-submission-protocol-for-microbial-pathogen-su-cspbwdin | Ruth Timme, Julie Haendiges, Tina.Pfefer, Errol Strain, Maria Balkey | TITLE: NCBI submission protocol for microbial pathogen surveillance
AUTHORS: Ruth Timme, Julie Haendiges, Tina.Pfefer, Errol Strain, Maria Balkey
[DESCRIPTION]
PURPOSE: Step-by-step instructions for submitting pathogen whole genome sequence data to NCBI and to the NCBI Pathogen Detection portal. This protocol covers ... | ["[Establish submission environmnet at NCBI] Set up a new NCBI submission environment for your lab:\n\n1.1: Create an NCBI user account\n1.2: Set up an NCBI submission user group for your lab\n1.4: Bookmark the link to your submission portal\n1.5. Identify or establish new BioProjects (detailed in Step 3)\n\n\nReady fo... |
41,925 | mr test | 1 | null | https://www.protocols.io/view/mr-test-bk7dkzi6 | Mariia | TITLE: mr test
AUTHORS: Mariia
[STEPS]
?. test
?. test 1 | ["test", "test 1"] |
63,408 | Aktiv Formulations Keto BHB 100% Safe And Effective Formulation!(Legit Or Scam?) | 3 | dx.doi.org/10.17504/protocols.io.kxygxz2ekv8j/v1 | https://www.protocols.io/view/aktiv-formulations-keto-bhb-100-safe-and-effective-b96qr9dw | ninjasaifox | TITLE: Aktiv Formulations Keto BHB 100% Safe And Effective Formulation!(Legit Or Scam?)
AUTHORS: ninjasaifox
[DESCRIPTION]
Aktiv Formulations Keto BHB
[STEPS] | [] |
34,904 | Comparative risk of hypophosphatemia following the administration of intravenous iron preparations: a network meta-analysis | null | dx.doi.org/10.17504/protocols.io.bebyjapw | null | Ioannis Bellos | TITLE: Comparative risk of hypophosphatemia following the administration of intravenous iron preparations: a network meta-analysis
AUTHORS: Ioannis Bellos
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The administration of intravenous iron has been recently linked to increased risk of hypophosphat... | ["Review title: Comparative risk of hypophosphatemia following the administration of intravenous iron preparations: a network meta-analysis", "Review question: To compare the incidence of hypophosphatemia following the intravenous administration of different iron preparations (ferric carboxymaltose, ferumoxytol, iron i... |
24,351 | Translation and cultural adaptation of Lithuanian version of the anterior cruciate ligament return to sport after injury (ACL-RSI) scale | null | dx.doi.org/10.17504/protocols.io.3z7gp9n | null | Saulė Salatkaitė, Laimonas Šiupšinskas, Rimtautas Gudas | TITLE: Translation and cultural adaptation of Lithuanian version of the anterior cruciate ligament return to sport after injury (ACL-RSI) scale
AUTHORS: Saulė Salatkaitė, Laimonas Šiupšinskas, Rimtautas Gudas
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Purpose </div><div class = "text-block">To ... | ["[Permission]\nReceived the authors' agreement to use and translate ACL-RSI scale.", "[Translation]\nScale was translated by physical therapist and translator who were all native Lithuanian speakers and fluent in English.", "[Translation]\nTranslators discussed about translations.", "[Translation]\nA common Lithuanian... |
47,471 | Brucella species detection from blood and milk samples | 4 | dx.doi.org/10.17504/protocols.io.bskpncvn | https://www.protocols.io/view/brucella-species-detection-from-blood-and-milk-sam-bskpncvn | Rania Baleela, Zienab Adam Ahmed Abdallh | TITLE: Brucella species detection from blood and milk samples
AUTHORS: Rania Baleela, Zienab Adam Ahmed Abdallh
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify">Brucellosis is a widespread zoonotic disease which is characterized by </div><style>
... | ["[DNA extraction: The phenol / chloroform method was used to extract genomic DNA.]\nWash 1ml of blood with Red Blood Cells lysis buffer (NaHCO3 0.0841g, NH4Cl6.15135g 1000ml distilled water) twice centrifuge at 60000 rpm for 5min", "[DNA extraction: The phenol / chloroform method was used to extract genomic DNA.]\nS... |
98,671 | Fecal Carmine Red Protocol | 0 | dx.doi.org/10.17504/protocols.io.eq2lywpwwvx9/v1 | https://www.protocols.io/view/fecal-carmine-red-protocol-dckp2uvn | Adam Hamilton, Ian N Krout, Tim Sampson | TITLE: Fecal Carmine Red Protocol
AUTHORS: Adam Hamilton, Ian N Krout, Tim Sampson
[DESCRIPTION]
This assay is used to determine whole gut transit time. Mice are given an oral gavage containing a known volume of bright red carmine dye. Mice are placed into empty cages and are then observed in 15-minute intervals unti... | ["[Pre-protocol] Prepare Carmine Red Soln. (see materials)", "[Pre-protocol] Autoclave Carmine Red Soln. if sterility is required. (i.e. microbiome analysis)", "[Pre-protocol] Shake well or stir on low heat to homogenize", "[Pre-protocol] Once resuspended, immediately aliquot into 1.5 mL tubes and store in fridge to pr... |
37,753 | 20% Paraformaldehyde in 5X PBS | 1 | dx.doi.org/10.17504/protocols.io.bg4zjyx6 | https://www.protocols.io/view/20-paraformaldehyde-in-5x-pbs-bg4zjyx6 | Allen Institute for Brain Science | TITLE: 20% Paraformaldehyde in 5X PBS
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used to prepare 20% Paraformaldehyde (PFA) in 5X Phosphate-buffered saline (PBS). 20% PFA in 5X PBS is utilized to make the 4% PFA in 1X PBS reagent.</div... | [] |
53,198 | WORKFLOW FOR THE NUCLEIC ACID BASED IDENTIFICATION OF INSECTS USING WHOLE GENOME AMPLIFICATION AND NANOPORE SEQUENCING - Monarch® | 1 | dx.doi.org/10.17504/protocols.io.bx7nprme | https://www.protocols.io/view/workflow-for-the-nucleic-acid-based-identification-bx7nprme | Jürg E Frey, Beatrice Frey, Daniel Frei, Morgan Gueuning, Simon Blaser, Andreas Bühlmann | TITLE: WORKFLOW FOR THE NUCLEIC ACID BASED IDENTIFICATION OF INSECTS USING WHOLE GENOME AMPLIFICATION AND NANOPORE SEQUENCING - Monarch®
AUTHORS: Jürg E Frey, Beatrice Frey, Daniel Frei, Morgan Gueuning, Simon Blaser, Andreas Bühlmann
[DESCRIPTION]
BACKGROUND
World-wide trade with plant material has dramaticall... | ["[1 Sample preparation and DNA Extraction - 1.1 Tissue Disruption] Materials: \n\nDisrupt tissue samples on the Retsch Mixer Mill TissueLyser II (Qiagen), using the Monarch® Genomic DNA Purification Kit (New England Biolabs NEB #T3010) and Qiagen Collection Microtubes (racked) and Collection Microtube Caps (cat. nos. ... |
21,973 | Participants’ recruitment and samples collection | null | dx.doi.org/10.17504/protocols.io.zpvf5n6 | null | Barbara Rizzacasa, Elena Morini, Ruggiero Mango, Chiara Vancheri, Simone Budassi, Gianluca Massaro, Sara Maletta, Massimiliano Macrini, Silvio D’Annibale, Francesco Romeo, Giuseppe Novelli, Francesca Amati | TITLE: Participants’ recruitment and samples collection
AUTHORS: Barbara Rizzacasa, Elena Morini, Ruggiero Mango, Chiara Vancheri, Simone Budassi, Gianluca Massaro, Sara Maletta, Massimiliano Macrini, Silvio D’Annibale, Francesco Romeo, Giuseppe Novelli, Francesca Amati
[DESCRIPTION]
<div class = "text-blocks"><div cl... | ["[Partecipant's recruitment]\nA total of 99 patients has been enrolled for our study: 61 patients with chronic stable coronary artery disease (CAD) and 38 patients after a myocardial infarction event (AMI). For each patient, we took a blood sample.", "[Sample collection]\n•\t10mL of whole blood have been collected in ... |
65,663 | Monkeypox virus whole genome sequencing using combination of NextGenPCR and Oxford Nanopore | 4 | null | https://www.protocols.io/view/monkeypox-virus-whole-genome-sequencing-using-comb-ccc7sszn | Matthijs Welkers, M. Jonges, Anton van den Ouden | TITLE: Monkeypox virus whole genome sequencing using combination of NextGenPCR and Oxford Nanopore
AUTHORS: Matthijs Welkers, M. Jonges, Anton van den Ouden
[DESCRIPTION]
Rapid genomic surveillance of monkeypox virus (MPXV) can provide valuable insights in order to guide public health interventions. Current sequen... | ["[Primer pool preparation] If required, resuspend lyophilised primers to a concentration of 100µM each", "[Multiplex PCR] Add 5 µL of each DNA sample to the NextGenPCR microplate containing 15 µL Pool 1. Mix well by pipetting\nAdd 5 µL of each DNA sample to the NextGenPCR microplate containing 15 µL Pool 2. Mix well... |
108,480 | JGI/LBNL Metabolomics - Standard LC-MS/MS ESI Method - Polar HILIC-Z | 1 | dx.doi.org/10.17504/protocols.io.kxygxydwkl8j/v1 | https://www.protocols.io/view/jgi-lbnl-metabolomics-standard-lc-ms-ms-esi-method-dm6849hw | Katherine B. Louie, Suzanne Kosina, Thomas Harwood, Meghana Faltane, Marie Lynde, Benjamin P. Bowen, Trent Northen | TITLE: JGI/LBNL Metabolomics - Standard LC-MS/MS ESI Method - Polar HILIC-Z
AUTHORS: Katherine B. Louie, Suzanne Kosina, Thomas Harwood, Meghana Faltane, Marie Lynde, Benjamin P. Bowen, Trent Northen
[DESCRIPTION]
This protocol describes the standard LC-MS/MS ESI method developed at Lawrence Berkeley National Laborato... | ["[Mass Spectrometer Preparation] Prior to data acquisition, the mass spectrometer is calibrated using standard calibration procedures available in the Thermo XCalibur operating software. ESI needle position is optimized relative to the source to achieve stable and acceptable ion intensity levels.\n\nCalibration proce... |
28,587 | E. coli transformation | null | dx.doi.org/10.17504/protocols.io.76jhrcn | null | iGEM Dusseldorf | TITLE: E. coli transformation
AUTHORS: iGEM Dusseldorf
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><ul style = "list-style-type:disc;"><li style = "counter-reset:ol0;list-style-type:disc;">Take tubes with 50 µL of TOP10F’ competent cells from -80°C freezer and place on ice.</li><li style = "coun... | [] |
103,083 | Purification of mCherry-ATG101/13 (1-191aa) subcomplex | 0 | dx.doi.org/10.17504/protocols.io.n92ld8wo9v5b/v1 | https://www.protocols.io/view/purification-of-mcherry-atg101-13-1-191aa-subcompl-dgwj3xcn | Elias Adriaenssens | TITLE: Purification of mCherry-ATG101/13 (1-191aa) subcomplex
AUTHORS: Elias Adriaenssens
[DESCRIPTION]
This protocol details the purification of mCherry-ATG101/13 (1-191aa) subcomplex.
[STEPS]
SECTION: Purification - mCherry-ATG101/13 (1-191aa) subcomplex
1. To purify mCherry-ATG13/101 HORMA dimer, we express mCherr... | ["[Purification - mCherry-ATG101/13 (1-191aa) subcomplex] To purify mCherry-ATG13/101 HORMA dimer, we express mCherry-tagged ATG13 (1-191aa) from a pCAG backbone (available from Addgene) together with GST-TEV-ATG101 (available from Addgene).", "[Purification - mCherry-ATG101/13 (1-191aa) subcomplex] Express the ATG13/1... |
41,711 | PCR-cDNA Barcoding (SQK-PCB109) | 4 | dx.doi.org/10.17504/protocols.io.bkypkxvn | https://www.protocols.io/view/pcr-cdna-barcoding-sqk-pcb109-bkypkxvn | Oxford Nanopore Technologies | TITLE: PCR-cDNA Barcoding (SQK-PCB109)
AUTHORS: Oxford Nanopore Technologies
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Barcoding or multiplexing is useful when the amount of data required per sample is less than the total amount of data that can be generated from a single flow cell: it allows ... | ["[Reverse transcription and strand-switching]\nMix gently by flicking the tube, and spin down.", "[Reverse transcription and strand-switching]\nPrepare the following reaction in a 0.2 ml PCR tube:", "[Reverse transcription and strand-switching]\nIncubate at 65° C for 5 minutes and then snap cool on a pre-chilled freez... |
15,260 | PCC559 medium | null | dx.doi.org/10.17504/protocols.io.s54eg8w | null | Roscoff Culture Collection | TITLE: PCC559 medium
AUTHORS: Roscoff Culture Collection
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Pasteur Collection medium for cyanobacteria (</span><span style = "font-style:italic;">Prochlorococcus</span><span>, </span><span style = "font-style:italic;">Synechococcus</span><span>).</... | ["[Medium composition]\nUnder hood, add these nutriments autoclaved before (excepted vitamin): Quantity\n Compound\n 1 L\n Turks Island Salts 1X\n 4 mL\n Ferric chloride hexahydrate/EDTA solution\n 1mL\n Trace metal for Prochlorococcus medium\n 1 mL\n Na-PO4 solution (50 mM, pH 7.5)\n ... |
89,205 | Troubleshooting guide for DDNS V2 | 3 | dx.doi.org/10.17504/protocols.io.8epv5xe84g1b/v1 | https://www.protocols.io/view/troubleshooting-guide-for-ddns-v2-c3cvyiw6 | Joyce Akello, Alex Shaw, Catherine Troman, Erika Bujaki, Manasi Majumdar, Aine.OToole, c.ansley, Zoe Vance, rachel.colquhoun, Andrew Rambaut, Javier Martin, Nick Grassly | TITLE: Troubleshooting guide for DDNS V2
AUTHORS: Joyce Akello, Alex Shaw, Catherine Troman, Erika Bujaki, Manasi Majumdar, Aine.OToole, c.ansley, Zoe Vance, rachel.colquhoun, Andrew Rambaut, Javier Martin, Nick Grassly
[DESCRIPTION]
This document provides general guidance for troubleshooting problems encountered in ... | [] |
31,552 | Simplified protocol for Agrobacterium-mediated transformation of the liverwort Marchantia polymorpha, includes protocols for spore sterilisation | null | dx.doi.org/10.17504/protocols.io.ba28ighw | null | Suvi Honkanen, Victor A. S. Jones | TITLE: Simplified protocol for Agrobacterium-mediated transformation of the liverwort Marchantia polymorpha, includes protocols for spore sterilisation
AUTHORS: Suvi Honkanen, Victor A. S. Jones
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Simplified protocol for Agrobacterium-mediated transforma... | [] |
25,310 | Marchantia chloroplast isolation | null | dx.doi.org/10.17504/protocols.io.4x6gxre | null | Eftychis Frangedakis | TITLE: Marchantia chloroplast isolation
AUTHORS: Eftychis Frangedakis
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is a modifiction of the </span><span style = "font-weight:bold;">ISOLATION OF MAIZE CHLOROPLASTS FOR PROTEIN IMPORT STUDIES </span><span>
protocl from Mark Sett... | ["Prepare 20 ml 30% Percoll solution by mixing 6ml Percoll, 14ml Buffer GR.", "Prepare 10 ml 70% Percoll solution by mixing 7ml Percoll and 3ml Buffer GR.", "Add 15ml of 30% Percoil soution in a 50ml Falcon tube. Very carefully underlay 6ml of 70% (denser) Percoll solution using a 5ml Gilson pipette (A in Figure).", "K... |
81,179 | Methodology for TFP Bioeconomy Impact post Covid-19 on the agricultural economy | 1 | dx.doi.org/10.17504/protocols.io.q26g7yeo3gwz/v1 | https://www.protocols.io/view/methodology-for-tfp-bioeconomy-impact-post-covid-1-cth3wj8n | C A Zuniga-Gonzalez | TITLE: Methodology for TFP Bioeconomy Impact post Covid-19 on the agricultural economy
AUTHORS: C A Zuniga-Gonzalez
[DESCRIPTION]
Methods: The panel data was organized with FAO Statistic data. Linear programming with an enveloping data analysis (DEA) approach was used to measure the Malmquist TFP indices to determine ... | ["[Methodology for TFP Bioeconomy Impact post Covid-19 on the agricultural economy] Panel Data. The data was organized from the statistic FAO in panel data. These variables are Value Agriculture (VAit), Land use (LUit), Unit Capital Stock (UCSit), Annual population (APit), Trade Indices (TIit), Consumer Prices, and Fo... |
91,550 | Nuclei preparation from frozen tissue for Chromium Single Cell Multiome ATAC + Gene Expression (10x Genomics) | 4 | dx.doi.org/10.17504/protocols.io.rm7vzx242gx1/v1 | https://www.protocols.io/view/nuclei-preparation-from-frozen-tissue-for-chromium-c5m6y49e | nzemke, Bing Ren | TITLE: Nuclei preparation from frozen tissue for Chromium Single Cell Multiome ATAC + Gene Expression (10x Genomics)
AUTHORS: nzemke, Bing Ren
[DESCRIPTION]
This protocol details nuclei preparation from frozen tissue for Chromium Single Cell Multiome ATAC + Gene Expression (10x Genomics). Tissue collection for this p... | ["[Nuclei preparation] Prechill any tubes, buffers or tools. Set the centrifuge to 4 °C.", "[Nuclei preparation] For each sample to be homogenized, prepare a Dounce Tissue Grinder with 2 pestles (“Loose” and “Tight”). Remove from 70% ethanol storage, rinse with MilliQ water three times. Place mortars (buckets) in ice. ... |
40,468 | Immunoblot analyses for investigating SpLG-binding to purified mammalian and avian immunoglobulins. | 6 | dx.doi.org/10.17504/protocols.io.bjrukm6w | https://www.protocols.io/view/immunoblot-analyses-for-investigating-splg-bindin-bjrukm6w | Angel Justiz-Vaillant | TITLE: Immunoblot analyses for investigating SpLG-binding to purified mammalian and avian immunoglobulins.
AUTHORS: Angel Justiz-Vaillant
[STEPS]
?. Aliquots of egg yolks, sera or 2 µg/µl of purified immunoglobulins from birds, laboratory, wild, farm animals and pets are applied to the gels of SDS-PAGE as described ... | ["Aliquots of egg yolks, sera or 2 µg/µl of purified immunoglobulins from birds, laboratory, wild, farm animals and pets are applied to the gels of SDS-PAGE as described elsewhere.", "Gels are transferred to nitrocellulose membranes (Immobilon-Nc, pore size 0.45 µm, Sigma-Aldrich Co, St Louis, Missouri) during 75 minut... |
80,039 | Step by Step from Environmental Samples to Preservation Vials | 4 | dx.doi.org/10.17504/protocols.io.n2bvj8mk5gk5/v1 | https://www.protocols.io/view/step-by-step-from-environmental-samples-to-preserv-csefwbbn | phangguanjie | TITLE: Step by Step from Environmental Samples to Preservation Vials
AUTHORS: phangguanjie
[DESCRIPTION]
This protocol shows how to generate a MICROBES ISOLATION FROM ENVIRONMENTAL SAMPLES into LAB COLLECTION. Please follow the instructions and do not modify the protocols by yourself. If any changes are needed please ... | ["[Isolate Primary Culture from Environmental Samples] Once you received your environmental samples. \n\nPlease catalog them in your Environmental Samples spreadsheet.", "[Upload your datasheet to Specify database] **The account setup is skipped**\n\nLogin to the Specify database. Choose the first collection (HuangLab-... |
105,012 | Evercode Dual Index PCR | 0 | dx.doi.org/10.17504/protocols.io.yxmvmeqe5g3p/v1 | https://www.protocols.io/view/evercode-dual-index-pcr-disu4eew | Elisabeth Rebboah, Parse Biosciences | TITLE: Evercode Dual Index PCR
AUTHORS: Elisabeth Rebboah, Parse Biosciences
[DESCRIPTION]
This protocol describes the dual-index PCR procedure for Parse Biosciences Evercode WT and WT Mega v2 kits. Each subpool is barcoded with two Illumina indices on the 5' and 3' ends of the cDNA library. These indices acts as the ... | ["[Sublibrary Dual Index PCR] If using the alternative version of Evercode Mega WT v2 (ECW02050) that includes RX100 instead of RX200, follow the protocol modifications described in Appendix D.\n\nMultiple thermocyclers may be needed for this section depending on the amount of cDNA added to each sublibrary during the f... |
61,423 | Plasmid-reprogramming of human fibroblasts | 4 | dx.doi.org/10.17504/protocols.io.eq2lyn8qwvx9/v1 | https://www.protocols.io/view/plasmid-reprogramming-of-human-fibroblasts-b78prrvn | Pascale Baden, michela.deleidi | TITLE: Plasmid-reprogramming of human fibroblasts
AUTHORS: Pascale Baden, michela.deleidi
[DESCRIPTION]
This protocol details about plasmid-reprogramming of human fibroblasts.
[GUIDELINES]
Adapted from Okita et al PMID: 21460823.
[STEPS]
SECTION: Nucleofection (Day 0)- with Amaxa Nucleofector I/II
1. Prepare nucleof... | ["[Nucleofection (Day 0)- with Amaxa Nucleofector I/II] Prepare nucleofection solution: \n Human Dermal Fibroblast Nucleofector solution 82 µL Supplement 18 µl Plasmid 10 µg", "[Nucleofection (Day 0)- with Amaxa Nucleofector I/II] Nucleofect 700.000 fibroblasts (resuspended in the nucleofection soluti... |
58,940 | Colony PCR for screening transgenic Ostreococcus tauri | 4 | dx.doi.org/10.17504/protocols.io.b5s4q6gw | https://www.protocols.io/view/colony-pcr-for-screening-transgenic-ostreococcus-t-b5s4q6gw | Shikha Adhikari, Faith Losbanes, Anbarasu Karthikaichamy | TITLE: Colony PCR for screening transgenic Ostreococcus tauri
AUTHORS: Shikha Adhikari, Faith Losbanes, Anbarasu Karthikaichamy
[DESCRIPTION]
Colony PCR protocol for screening transgenic Ostreococcus tauri
[STEPS]
1. Measure cell concentration using a hemocytometer. Ideally, the cell concentration should be around... | ["Measure cell concentration using a hemocytometer. Ideally, the cell concentration should be around 1-2x10^5 cells/ml", "Mix 50 µL of cells and 50 µL sterile water in a PCR tube.", "Boil the PCR tube at 95 °C for 5 min in a thermocycler.", "After boiling, briefly centrifuge the PCR tube. Use 1 µL from the boiled sampl... |
56,552 | Immunohistochemistry/Immunofluorescence | 4 | null | https://www.protocols.io/view/immunohistochemistry-immunofluorescence-b3ggqjtw | Michael Henderson | TITLE: Immunohistochemistry/Immunofluorescence
AUTHORS: Michael Henderson
[DESCRIPTION]
This protocol details about the immunohistochemisty/immunofluorescence staining techniques for tissue.
[STEPS]
SECTION: Day 1
1. Label slides with antibody and treatment to be used.
SECTION: Day 1
2. De-paraffinize slides in fresh... | ["[Day 1] Label slides with antibody and treatment to be used.", "[Day 1] De-paraffinize slides in fresh xylenes, then in a descending ethanol series.", "[Day 1] Formic Acid Retrieval (If necessary, do here).", "[Day 1] Microwave antigen retrieval (CA; If necessary do here).", "[Day 1] Immerse in freshly prepared Metha... |
35,150 | Sucrose Gradient_Surface Isolation | 1 | dx.doi.org/10.17504/protocols.io.rm7vz81m2vx1/v1 | https://www.protocols.io/view/sucrose-gradient-surface-isolation-bejnjcme | Alexander Radaoui, hamiltonak, Karina L Conkrite | TITLE: Sucrose Gradient_Surface Isolation
AUTHORS: Alexander Radaoui, hamiltonak, Karina L Conkrite
[DESCRIPTION]
Protocol for extracting the surface membrane of cell lines or PDX tumors (or patient tumors) and preparing for mass spec.
[STEPS]
SECTION: DAY 1
1. After all buffers are prepared, retrieve PDX/tumor samp... | ["[DAY 1] After all buffers are prepared, retrieve PDX/tumor samples or cells and thaw on ice. Add 1 tablet of Roche cOmplete™Protease Inhibitor Cocktail EASYpack per 50 mL of homogenization buffer. Vortex to dissolve tablet.\nFor cells, aim to have roughly 100 million.\nFor solid PDX tumor, aim to have between 250 and... |
47,281 | Recombinant expression and purification of codon-optimized M-MLV and Mashup | 4 | dx.doi.org/10.17504/protocols.io.bsernbd6 | https://www.protocols.io/view/recombinant-expression-and-purification-of-codon-o-bsernbd6 | Maira Rivera, Javiera Reyes, Paula Blazquez-Sanchez, Cesar A Ramirez-Sarmiento | TITLE: Recombinant expression and purification of codon-optimized M-MLV and Mashup
AUTHORS: Maira Rivera, Javiera Reyes, Paula Blazquez-Sanchez, Cesar A Ramirez-Sarmiento
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol has been optimized for the recombinant expression of codon-optizime... | ["[DAY 1 – Plasmid transformation]\nTransform of plasmid containing codon-optimized M-MLV or Mashup into E. coli BL21(DE3) competent cells using either heat shock or electroporation.\n100 ng", "[DAY 1 – Plasmid transformation]\nSpread transformed cells in LB Agar plates supplemented with Kan for Mashup, or Amp for M-M... |
4,686 | Extraction of total RNA from E. coli cells | null | dx.doi.org/10.17504/protocols.io.gtnbwme | null | Alice Pawlowski | TITLE: Extraction of total RNA from E. coli cells
AUTHORS: Alice Pawlowski
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The protocol is used for the extraction of total RNA from </span><span style = "font-style:italic;">E. coli</span><span> cells. It is based on the method described by Chom... | ["[stop of RNA synthesis]\nwork under the hoodmix 1 ml of cells with 200 µl 'stopmix'- solution (5 % phenol in ethanol) in a 2 ml safe lock tube tube → stops RNA production in the cellscentrifuge for 5 min at 4°C and 14000 x gdiscard the supernatant and resuspend the pellet in 1 ml NucleoZOL (Macherey and Nagel), plac... |
79,840 | Marine mammal sex determination using epidermal tissue recovered from suction-cup tags | 4 | dx.doi.org/10.17504/protocols.io.5qpvor42dv4o/v1 | https://www.protocols.io/view/marine-mammal-sex-determination-using-epidermal-ti-cr78v9rw | Sadie Novak, Jacob MJ Linsky, Kaitlyn J Knapp, Susan Parks, David Wiley, Dana Cusano | TITLE: Marine mammal sex determination using epidermal tissue recovered from suction-cup tags
AUTHORS: Sadie Novak, Jacob MJ Linsky, Kaitlyn J Knapp, Susan Parks, David Wiley, Dana Cusano
[DESCRIPTION]
For many marine mammal species, minimal sexual dimorphism means that sex cannot be reliably identified through observ... | ["[Field Sampling] Retrieve the tag from the water. While retrieving the tag, ensure that nothing touches the suction cups with the exception of the net used for retrieval and wear gloves to prevent contamination.", "[Field Sampling] Using fresh nitrile gloves, wipe the inside of the suction cups with a sterile swab, a... |
20,207 | Fungal gene knockout with Agrobacterium tumefaciens using Gibson assembly | 1 | null | https://www.protocols.io/view/fungal-gene-knockout-with-agrobacterium-tumefacien-xypfpvn | Johannes Wolfram Debler | TITLE: Fungal gene knockout with Agrobacterium tumefaciens using Gibson assembly
AUTHORS: Johannes Wolfram Debler
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This method uses Agrobacterium tumefaciens to transfer a piece of TDNA containing a resistance gene (hph for hygromycin in this particular... | ["[PCR of flanking regions]\nDepending on your fungal organism you may have to try different sizes. A good starting length is 1000 bp up- and downstream of your gene of interest.Use a proof reading polymerase!The primers we use to amplify the 5'- and 3' UTRs will carry tails which overlap with our plasmid backbone and ... |
90,791 | ColorBones: Full step-by-step protocol for the visualization and identification of bone discolorations using the ImageJ© plugin DStretch® | 1 | dx.doi.org/10.17504/protocols.io.4r3l22ybxl1y/v1 | https://www.protocols.io/view/colorbones-full-step-by-step-protocol-for-the-visu-c4wfyxbn | Dominik Göldner | TITLE: ColorBones: Full step-by-step protocol for the visualization and identification of bone discolorations using the ImageJ© plugin DStretch®
AUTHORS: Dominik Göldner
[DESCRIPTION]
Fresh, undecayed, and healthy bone in animals and humans typically exhibits a greasy, yellowish-white to yellowish-brown color (Dupras ... | ["[Preparation phase] Camera setup: \n\nPrepare your camera and accessories by charging and cleaning them before use. If available, regularly use the digital image sensor cleaning function of your camera. \n\nDSLR cameras, known for producing less image noise, contribute to overall better image enhancement quality. Opt... |
83,237 | Generation of stable ATG3-mCherry wild-type or mutans HeLa cells with HaloTag-LC3B using lentivirus | 4 | dx.doi.org/10.17504/protocols.io.dm6gp3exjvzp/v1 | https://www.protocols.click/view/generation-of-stable-atg3-mcherry-wild-type-or-mut-cvidw4a6 | Xuefeng Ren | TITLE: Generation of stable ATG3-mCherry wild-type or mutans HeLa cells with HaloTag-LC3B using lentivirus
AUTHORS: Xuefeng Ren
[DESCRIPTION]
This protocol details the generation of stable ATG3-mCherry wild-type or mutant HeLa cells with HaloTag-LC3B using lentivirus.
[STEPS]
SECTION: Cloning pCDH1-CMV-ATG3-mCherry-H... | ["[Cloning pCDH1-CMV-ATG3-mCherry-Hygro lentiviral vector (ATG3 wild-type or mutants)] Amplify the coding sequence for human ATG3 (1-125), mCherry or ATG3 (126-314) fragment using Q5 High Fidelity DNA Polymerase and purify PCR products using Gel extraction kit (Bio Basic).", "[Cloning pCDH1-CMV-ATG3-mCherry-Hygro lenti... |
null | null | null | dx.doi.org/10.17504/protocols.io.den3dd | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
Before performing a one-step experiment, you must have documented three consecutive days of consistent growth curves for the host.<br /><br /><strong>Host growth curve:<br /></strong><br />1.) Inoculate a new culture 1:100; i.e., transfer 80 μl from yesterday’s culture to a new ... | [] |
36,820 | Quick Protocol for Monarch® DNA Gel Extraction Kit (NEB #T1020) | 1 | dx.doi.org/10.17504/protocols.io.bf7ujrnw | https://www.protocols.io/view/quick-protocol-for-monarch-dna-gel-extraction-kit-bf7ujrnw | New England Biolabs | TITLE: Quick Protocol for Monarch® DNA Gel Extraction Kit (NEB #T1020)
AUTHORS: New England Biolabs
[DESCRIPTION]
This is the quick version of the Monarch® DNA Gel Extraction Kit Protocol (NEB #T1020). For the full protocol, please click here.
[BEFORE_START]
Add 4 volumes of ethanol (≥ 95%) to one volume of DNA Wash ... | ["Excise the DNA fragment from the agarose gel, taking care to trim excess agarose. Transfer to a 1.5 ml microfuge tube and weigh the gel slice. Minimize exposure to UV light.", "Add 4 volumes of Gel Dissolving Buffer to the gel slice (e.g., 400 μl buffer per 100 μl or 100 mg agarose).", "Incubate the sample between 37... |
80,899 | Measuring Turbidity and Fish Populations around Mo'orea | 1 | null | https://www.protocols.io/view/measuring-turbidity-and-fish-populations-around-mo-cs9bwh2n | Ellis Gelt | TITLE: Measuring Turbidity and Fish Populations around Mo'orea
AUTHORS: Ellis Gelt
[DESCRIPTION]
The ocean is often viewed as a fridge or pantry for many island communities, especially that of Mo’orea, French Polynesia. But, it's known that sedimentation can cause coral death, and corals are vital places for reef... | ["[GRID CONSTRUCTION] lay out buoys in a 6x6 grid each a meter apart (5 meters squared)", "[GRID CONSTRUCTION] cut rope into 12 pieces of equal length", "[GRID CONSTRUCTION] tie rope to each buoy in every row of buoys vertically", "[GRID CONSTRUCTION] repeat for each row of buoy horizontally", "[FIELD] arrive to sample... |
65,358 | Ocuprime Does it really work? Review After 30 Days Use | 3 | dx.doi.org/10.17504/protocols.io.6qpvr6ym3vmk/v1 | https://www.protocols.io/view/ocuprime-does-it-really-work-review-after-30-days-cb3nsqme | Ocuprime | TITLE: Ocuprime Does it really work? Review After 30 Days Use
AUTHORS: Ocuprime
[DESCRIPTION]
MUST CHECK: *Special Discounted Pricing Available For The First 50 Customers Only! (ORDER Ocuprime Vision Support)
[STEPS] | [] |
47,029 | Action Spectra protocol for Opentrons OT-1 liquid handling robot | 4 | dx.doi.org/10.17504/protocols.io.br6vm9e6 | https://www.protocols.io/view/action-spectra-protocol-for-opentrons-ot-1-liquid-br6vm9e6 | andrei.herdean | TITLE: Action Spectra protocol for Opentrons OT-1 liquid handling robot
AUTHORS: andrei.herdean
[STEPS]
?. OT-1 setup: A3 - box with 1 ml tips B3 - 48 well plate 1D3 - 48 well plate 2C1 - 48 well plate 348 plate 1 setup: C8 - oxygen optode D8 - temperature sensor A7, B7, C7, D7, E7, F7 - blank media F... | ["OT-1 setup: A3 - box with 1 ml tips B3 - 48 well plate 1D3 - 48 well plate 2C1 - 48 well plate 348 plate 1 setup: C8 - oxygen optode D8 - temperature sensor A7, B7, C7, D7, E7, F7 - blank media F4, F5, F6 - ddH2O A8, B8, E8, F8 - empty All other wells have 1 ml of algae culture48 plate 2 se... |
98,520 | Small molecules released from islets of Langerhans determined by liquid chromatography – mass spectrometry | 4 | dx.doi.org/10.17504/protocols.io.6qpvr6rnzvmk/v2 | https://www.protocols.io/view/small-molecules-released-from-islets-of-langerhans-dcfy2tpw | Emmanuel O. Ogunkunle, Matthew J. Donohue, Daniel J. Steyer, Damilola I. Adeoye, Wesley J. Eaton, Michael Roper | TITLE: Small molecules released from islets of Langerhans determined by liquid chromatography – mass spectrometry
AUTHORS: Emmanuel O. Ogunkunle, Matthew J. Donohue, Daniel J. Steyer, Damilola I. Adeoye, Wesley J. Eaton, Michael Roper
[DESCRIPTION]
Islets of Langerhans are the endocrine tissue within the pancreas that... | ["[Methods] Benzoyl chloride derivatization\n\nFor production of calibration curves, 100 µLof a standard mixture of small molecules (concentrations given in Section 3.3 in the original publication) in BSS was mixed with 50 µL of 100 mM sodium carbonate (pH 9.2) and 50 µL 2% BzCl (by volume in ACN). The mixture was vort... |
null | null | null | dx.doi.org/10.17504/protocols.io.kqpcvvn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Here we describe a protocol for generating 3D human intestinal tissues (called organoids) in vitro from humanpluripotent stem cells (hPSCs). To generate intestinal organoids, pluripotent stem cells are first differentiated into FOXA2(+)SOX17(+) endoderm by treating the cells ... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.f8ybrxw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Dengan melakukan import data teman-teman sesama peserta ke Gmail/Google Contacts, maka Anda dapat dengan mudah menghubungi teman-teman peserta lainnya, melalui telepon, SMS, WhatsApp, Telegram, maupun email.</p>
<p> </p>
<p>File yang dibutuhkan:</p>
<ol>
<li>File CSV Google C... | [] |
77,746 | Whole-cell radioligand binding for receptor internalization | 1 | dx.doi.org/10.17504/protocols.io.x54v9dz91g3e/v1 | https://www.protocols.io/view/whole-cell-radioligand-binding-for-receptor-inter-cp6svree | Angus Li, Samuel Liu, Rennica Huang, Seungkirl Ahn, Robert J Lefkowitz | TITLE: Whole-cell radioligand binding for receptor internalization
AUTHORS: Angus Li, Samuel Liu, Rennica Huang, Seungkirl Ahn, Robert J Lefkowitz
[DESCRIPTION]
This protocol details an experimental procedure used to generate results described in the manuscript Li, A., Liu, S., Huang, R., Ahn, S., & Lefkowitz, R. J. ... | ["[Day 1] Grow cells on 150 mm dish to ~70% confluency", "[Day 1] Wash twice with 10 mL PBS", "[Day 1] Detach cells with 1.5 mL trypsin-EDTA + 10.5 mL media. Trypsinize for 5 minutes and check under microscope for complete detachment; tap dish if necessary", "[Day 1] Count cells with hematocytometer and dilute collecte... |
91,478 | Transfection and validation of BK channel expressing HEK-293 cells for the study of miR-9 regulation. | 4 | dx.doi.org/10.17504/protocols.io.yxmvm3ek5l3p/v2 | https://www.protocols.io/view/transfection-and-validation-of-bk-channel-expressi-c5jwy4pe | Katherine Cordero Padilla, Gerardo L. Alvarado Monefledt, Adriel Guevarez-Galan, Hector G Marrero Hernandez, Mario E. Lloret-Torres, Cristina Velazquez Marrero | TITLE: Transfection and validation of BK channel expressing HEK-293 cells for the study of miR-9 regulation.
AUTHORS: Katherine Cordero Padilla, Gerardo L. Alvarado Monefledt, Adriel Guevarez-Galan, Hector G Marrero Hernandez, Mario E. Lloret-Torres, Cristina Velazquez Marrero
[DESCRIPTION]
Research has identified the... | ["[Cell Culture] Thaw cells and then plate them as follows:", "[Cell Culture] Resuspend in 1mL of modified DMEM media composed of Dulbecco’s modified Eagle’s medium (D5796, Milwaukee, WI, USA) with 10% fetal bovine serum (FBS), 2.52mM HEPES; 10 units and 10µg/mL of Penicillin/Streptomycin (Pen/Strep), and 1mM Na-pyruva... |
null | null | null | dx.doi.org/10.17504/protocols.io.itrcem6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Calibration procedure for functionally aligning inertial sensors fixed to the shanks, thighs, and trunk (e.g. sacrum, sternum). The movements were originally designed for analyzing skiing movements where the person is wearing ski boots. However, the same protocol can be apply... | [] |
106,445 | Viral Enumeration of EPS Samples Using Wet Mount Epifluorescence Microscopy | 0 | null | https://www.protocols.io/view/viral-enumeration-of-eps-samples-using-wet-mount-e-dj7m4rk6 | Madeline Bellanger, Pieter Visscher, Richard Allen White III | TITLE: Viral Enumeration of EPS Samples Using Wet Mount Epifluorescence Microscopy
AUTHORS: Madeline Bellanger, Pieter Visscher, Richard Allen White III
[DESCRIPTION]
Epifluorescence microscopy (EFM) has been the gold standard method for environmental viral enumeration for over 25 years. Currently, standard EFM method... | ["[Sample Collection and Cleaning] Tare a 1.5 mL low protein binding nuclease free tube on a top loading balance.", "[Sample Collection and Cleaning] Collect approximately 100 mg of mat using a scoopula or similar tool cleaned with 70% ethanol and transfer to the tube. Record the mass of the mat sample.", "[Sample Coll... |
26,709 | SPARC_Duke_PelotGrill_OT2-OD025340_PigVagusNerve_Morphology | 1 | dx.doi.org/10.17504/protocols.io.6bvhan6 | https://www.protocols.io/view/sparc-duke-pelotgrill-ot2-od025340-pigvagusnerve-m-6bvhan6 | Nicole A. Pelot, Gabriel B. Goldhagen, Jake E. Cariello, Warren M. Grill | TITLE: SPARC_Duke_PelotGrill_OT2-OD025340_PigVagusNerve_Morphology
AUTHORS: Nicole A. Pelot, Gabriel B. Goldhagen, Jake E. Cariello, Warren M. Grill
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The protocol describes image segmentation and image analysis methods to quantify pig vagus nerve morpho... | ["[Image Segmentation]\nWe used Nikon's NIS Elements software (v5.02.01, Build 1270) to segment pig vagus nerve micrographs stained with Masson's trichrome using the General Analysis RGB tool.", "[Image Segmentation]\nWe converted the binary segmented image into “Graticule Masks”, binary images saved as TIFs.", "[Image... |
37,651 | AutoCUT&Tag: streamlined genome-wide profiling of chromatin proteins on a liquid handling robot | 1 | dx.doi.org/10.17504/protocols.io.bgztjx6n | https://www.protocols.io/view/autocut-amp-tag-streamlined-genome-wide-profiling-bgztjx6n | Derek Janssens, Steven Henikoff | TITLE: AutoCUT&Tag: streamlined genome-wide profiling of chromatin proteins on a liquid handling robot
AUTHORS: Derek Janssens, Steven Henikoff
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The CUT&Tag method is based on antibody tethering of the Tn5 transposase to profile the genome-wide oc... | ["[Prepare Nuclei]\nObtain cells of interest and centrifuge at 600XG for 3 min in a 1.5 mL microfuge tube (if prepping nuclei from ≤ 1 million cells) or in a 15 mL conical tube if preparing cells in bulk.", "[Prepare Nuclei]\nCarefully remove the liquid and resuspend cells in 1 mL cold NE 1 Buffer per 1 million cells ... |
61,933 | PNA-lipophilic Ligand Conjugates Synthesis | 6 | dx.doi.org/10.17504/protocols.io.81wgb652qlpk/v1 | https://www.protocols.io/view/pna-lipophilic-ligand-conjugates-synthesis-b8qmrvu6 | Cathy Miller | TITLE: PNA-lipophilic Ligand Conjugates Synthesis
AUTHORS: Cathy Miller
[DESCRIPTION]
Lipophilic ligands are a class of substances suitable for cell transport, they are lipids with a certain hydrophilic-lipophilic balance. When transported across the cell membrane, the hydrophilic end faces the extracellular water-so... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.i6gchbw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Luria Broth (LB) is a nutrient-rich liquid media that is used to grow bacterial cultures. Luria Broth consists of Tryptone, Yeast extract and Sodium Chloride mixed into distilled water.</p>
[BEFORE_START]
<p>Give yourself about 2.5 hours to finish making the sterilized, read... | ["Read the instructions on the LB container to figure out how many grams per liter are needed to make liquid media.", "{\"blocks\":[{\"key\":\"43rri\",\"text\":\"Take the sterile spoon and spoon LB onto weigh tray.\\u00a0The LB powder is very fine so handle it slowly and with care. The dust can get all over the bench a... |
99,791 | VAMPseq Protocol | 0 | dx.doi.org/10.17504/protocols.io.4r3l2q77xl1y/v1 | https://www.protocols.io/view/vampseq-protocol-ddpp25mn | Raining Wang, Melinda Wheelock | TITLE: VAMPseq Protocol
AUTHORS: Raining Wang, Melinda Wheelock
[DESCRIPTION]
This protocol describes the materials and method to conduct an experiment of Variant Abundance by Massively Parallel sequencing (VAMP-seq) assay. There are two designation plasmids available for a gene of interest (GOI) to fuse with a EGFP r... | [] |
55,982 | Ancestral State Reconstruction | 5 | dx.doi.org/10.17504/protocols.io.6qpvr6e62vmk/v1 | https://www.protocols.io/view/ancestral-state-reconstruction-b2wnqfde | Dakota Betz | TITLE: Ancestral State Reconstruction
AUTHORS: Dakota Betz
[DESCRIPTION]
Our protocols are constantly evolving and old versions will be deleted.
The documents here are not intended to be cited in publications
[STEPS]
SECTION: Programs and Dependencies
1. Mesquite
Download: https://www.mesquiteproject.org/Installation... | ["[Programs and Dependencies] Mesquite\nDownload: https://www.mesquiteproject.org/Installation.html\n\nRAxML-ng\nDownload: https://github.com/amkozlov/raxml-ng\nGUI 2.0 (compatible with ng): https://antonellilab.github.io/raxmlGUI/\n\nFigTree\n\n\nText Editor (options below)\nSublimeText: https://www.sublimetext.com/3... |
null | null | null | dx.doi.org/10.17504/protocols.io.jhzcj76 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?. | [] |
71,706 | Optimized Grilled Cheese | 1 | dx.doi.org/10.17504/protocols.io.261ge3nx7l47/v1 | https://www.protocols.io/view/optimized-grilled-cheese-ch92t98e | Beth K. Martin, Chengxiang Qiu, Jay Shendure | TITLE: Optimized Grilled Cheese
AUTHORS: Beth K. Martin, Chengxiang Qiu, Jay Shendure
[DESCRIPTION]
Grilled Cheese Sandwiches are delicious. Here we describe a method for making an epic one.
(Submitted October 14, 2022, Happy Birthday Jay!)
[GUIDELINES]
Introduction
The Grilled Cheese Sandwich has been around for ... | ["[Bread Preparation] In the biggest mothereffing bowl that you can find, add the water, sugar, and yeast. Let sit for a few minutes until you see bubbles forming", "[Bread Preparation] Add the oil, salt, and 4 cups of flour. Stir until flour is incorporated, but you don't need to get all the lumps out.", "[Bread Prepa... |
60,843 | Mechanical colorectal stimuli for GCaMP6f characterization | 1 | dx.doi.org/10.17504/protocols.io.4r3l2o6p4v1y/v1 | https://www.protocols.io/view/mechanical-colorectal-stimuli-for-gcamp6f-characte-b7njrmcn | Tiantian Guo, Bin Feng | TITLE: Mechanical colorectal stimuli for GCaMP6f characterization
AUTHORS: Tiantian Guo, Bin Feng
[DESCRIPTION]
By adopting our developed high-throughput optical recording system, a large scale of dorsal root ganglia (DRG) neurons were recorded and identified from a whole DRG. Based on this custom-built platform, we f... | ["[Tissue preparation for GCaMP recording] Mice (VGU/GCaMP) 8-14 weeks of age were deeply anesthetized by intraperitoneal and intramuscular injection of a 0.4 mL cocktail of ketamine (120 mg/kg) and xylazine (10 mg/kg).", "[Tissue preparation for GCaMP recording] Mice were then euthanized by perfusion from the left ven... |
28,844 | Promega BacTiter-Glo Assay | null | dx.doi.org/10.17504/protocols.io.8ekhtcw | null | NUS iGEM | TITLE: Promega BacTiter-Glo Assay
AUTHORS: NUS iGEM
[STEPS]
?. Prepare BacTiter-Glo reagent mix by transferring BacTiter-Glo buffer into BacTiter-Glo substrate
These reagents are part of a set - Promega's BacTiter-Glo Assay.
?. Aliquot of cells into two wells of 96-well plate (duplicates)
50 µl
?. Add of BacTiter Gl... | ["Prepare BacTiter-Glo reagent mix by transferring BacTiter-Glo buffer into BacTiter-Glo substrate\nThese reagents are part of a set - Promega's BacTiter-Glo Assay.", "Aliquot of cells into two wells of 96-well plate (duplicates)\n50 µl", "Add of BacTiter Glo reagent mix into each well\n50 µl", "Include PBS-only well... |
88,551 | Buck Institute Morphology H & E staining protocol | 1 | dx.doi.org/10.17504/protocols.io.36wgq3n2ylk5/v3 | https://www.protocols.io/view/buck-institute-morphology-h-amp-e-staining-protoco-c2qfydtn | Stella Breslin, Akos A Gerencser | TITLE: Buck Institute Morphology H & E staining protocol
AUTHORS: Stella Breslin, Akos A Gerencser
[DESCRIPTION]
Histological Stain for FFPE slides
RESULTS: Nuclei-blue; Cytoplasm, red blood cells and connective tissue-shades of pink
[BEFORE_START]
Slides can be placed in 60 C oven prior to deparaffinization.
... | ["[Hematoxylin and Eosin Staining] Deparaffinization and rehydration: \n2 x xylene 7 min, \n100% ethanol 4 min, \n95% 4 min, \n80% 4 min, \n70% 4 min, \nbring to water.", "[Hematoxylin and Eosin Staining] Hematoxylin staining for 30 seconds - 4 min. using filtered dye (usually 2 mins) - Modified Mayes’s Hematoxylin HXM... |
37,976 | Separation of Human Neutrophils (PMN) from Buffy Coat | 1 | null | https://www.protocols.io/view/separation-of-human-neutrophils-pmn-from-buffy-coa-bhbyj2pw | Marco Cosentino, Elisa Storelli, Alessandra Luini, Emanuela Rasini, Massimiliano Legnaro, Marco Ferrari, Franca Marino | TITLE: Separation of Human Neutrophils (PMN) from Buffy Coat
AUTHORS: Marco Cosentino, Elisa Storelli, Alessandra Luini, Emanuela Rasini, Massimiliano Legnaro, Marco Ferrari, Franca Marino
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Separation of Human Neutrophils (PMN) from Buffy Coat: list of ... | ["Place 5 ml of venus blood from BUFFY COAT into 10 ml volume centrifuge tube.", "Add of Dextran solution and mix well drawing in and out of a pipette\n2 mL", "Incubate in the DARK for at\n37 °C", "Place of Fycoll-HyPaque media solution into a 10 ml volume centrifuge tube.\n3 mL", "Slowly and carefully layer the sup... |
50,604 | Link Github to Puhti | 5 | dx.doi.org/10.17504/protocols.io.bvnkn5cw | https://www.protocols.io/view/link-github-to-puhti-bvnkn5cw | Alise Ponsero | TITLE: Link Github to Puhti
AUTHORS: Alise Ponsero
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">How to connect your github account to a local machine or an HPC cluster (example at Puhti CSC)</div></div>
[STEPS]
?. [Verify that git is installed]
Open a terminal and log onto the remote machine (if... | ["[Verify that git is installed]\nOpen a terminal and log onto the remote machine (if applicable).In order to quickly test that Git is installed on the machine type:git --helpYou should have the git usage printed out!", "[Configuration of Github]\nTo configure the Git account type:git config --global user.name \"Your n... |
43,287 | Dundee peripheral blood mononuclear cell (PBMC) isolation protocol (from whole blood) | 4 | dx.doi.org/10.17504/protocols.io.bnhxmb7n | https://www.protocols.io/view/dundee-peripheral-blood-mononuclear-cell-pbmc-isol-bnhxmb7n | Adil R. Sarhan, Andrew J.M. Howden, Dario R. Alessi, Esther M. Sammler | TITLE: Dundee peripheral blood mononuclear cell (PBMC) isolation protocol (from whole blood)
AUTHORS: Adil R. Sarhan, Andrew J.M. Howden, Dario R. Alessi, Esther M. Sammler
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify">We describe a fast and effi... | ["Collect 3 x into BD Vacutainer sodium heparin 6ml tubes, green BD Hemogard Closure 13x100mm (BD, cat# 367876). Mix gently by inverting tubes 8 - 10 times.\n[blood]", "Add density gradient medium Ficoll-Paque PREMIUM to the SepMate™ tube (STEMCELL, Cat# 85450, 50 mL capacity) using a 20ml syringe with a large bore ne... |
36,020 | Preparation of TET Buffer | null | dx.doi.org/10.17504/protocols.io.bfeujjew | https://www.protocols.io/view/preparation-of-tet-buffer-bfeujjew | Nicola O'Reilly, Svend Kjaer, Maria Greco | TITLE: Preparation of TET Buffer
AUTHORS: Nicola O'Reilly, Svend Kjaer, Maria Greco
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Purpose of examination / Clinical relevance</span></div><div class = "text-block">At the end of 2019, several pneumonia cases were rep... | ["Please select between the recipes for 2 L TET and 5 L TET.", "Add to a 2 L single use cell culture bottle.\n[RNase free Water]", "Add , .\n[0.5 M EDTA]", "Add , .\n[1 M Tris-HCl]", "Add .\n[Tween-20]", "Make up to 2000 ml Water (RNAse free). Swirl very well to ensure that Tween-20 is well mixed in.", "Vacuum filter ... |
86,493 | Collection of human nasal cavity tissue at the time of autopsy and in preparation for routine microscopy. | 1 | null | https://www.protocols.io/view/collection-of-human-nasal-cavity-tissue-at-the-tim-cyp5xvq6 | Julianna Tomlinson, Nathalie Lengacher, Michael Schlossmacher | TITLE: Collection of human nasal cavity tissue at the time of autopsy and in preparation for routine microscopy.
AUTHORS: Julianna Tomlinson, Nathalie Lengacher, Michael Schlossmacher
[DESCRIPTION]
This protocol describes the collection of human nasal cavity tissue, including cribriform plate and olfactory and respira... | ["The body of the deceased has been transferred to the morgue at the Department of Pathology at participating hospitals and kept at 4ºC.", "Within an ideal post mortem interval of 4 and 48 hrs, and following the completion of consent forms that address the collection of the deceased person’s brain and/or other specifie... |
null | null | null | dx.doi.org/10.17504/protocols.io.j8ucrww | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Use this protocol to mask <em>Symbiodinium</em> cell surface glycans prior to colonizing aposymbiotic <em>Exaiptasia</em> polyps, then measure colonization dynamics with epifluorescent microscopy.</p>
[BEFORE_START]
<p>Several variables affect symbiont uptake rate, such as h... | [] |
32,723 | Quantification of Nitrogen and Phosphorus in grass and soil samples using ICP-OES | null | dx.doi.org/10.17504/protocols.io.bb7tirnn | null | Gabriel Mayengo, Gabriel Mayengo, Wolfgang Armbruster, Anna Treydte | TITLE: Quantification of Nitrogen and Phosphorus in grass and soil samples using ICP-OES
AUTHORS: Gabriel Mayengo, Gabriel Mayengo, Wolfgang Armbruster, Anna Treydte
[STEPS] | [] |
52,638 | Preparation of acute midbrain slices for patch-clamp recordings | 4 | dx.doi.org/10.17504/protocols.io.bxm6pk9e | https://www.protocols.io/view/preparation-of-acute-midbrain-slices-for-patch-cla-bxm6pk9e | Oriol Pavon Arocas, Tiago Branco | TITLE: Preparation of acute midbrain slices for patch-clamp recordings
AUTHORS: Oriol Pavon Arocas, Tiago Branco
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes two different approaches to prepare acute midbrain slices from young adult mice for slice electrophysiology experim... | ["[Preparation of stock solutions]\nThe protocol describes two different sets of solutions and two different methods for slicing. We have found that both the solutions (NMDG-HEPES slicing and HEPES holding) and the perfusion method with cold slicing ACSF used in PATH B significantly improve the quality of the slices an... |
90,653 | Multiplexed CRISPR-based target-enriched next-generation sequencing for detecting antibiotic resistance genes in environmental samples | 4 | dx.doi.org/10.17504/protocols.io.8epv5xdnjg1b/v1 | https://www.protocols.io/view/multiplexed-crispr-based-target-enriched-next-gene-c4r5yv86 | Yuqing Mao, Thanh H Nguyen | TITLE: Multiplexed CRISPR-based target-enriched next-generation sequencing for detecting antibiotic resistance genes in environmental samples
AUTHORS: Yuqing Mao, Thanh H Nguyen
[DESCRIPTION]
High-throughput detection of antibiotic resistance genes (ARGs) in complex environmental samples is challenging for two reasons... | ["[Guide RNA preparation] Mix the DNA template for either crRNA or tracrRNA, forward and corresponding\nreverse primers, Phusion High-Fidelity PCR Master Mix, and molecular biology\ngrade water in a nuclease-free PCR tube following the volumes listed in the\ntable below. Pipette up and down 10 times or until well mixed... |
90,813 | CRISPR nuclease (CRISPRn) genome editing | 1 | dx.doi.org/10.17504/protocols.io.dm6gp35qpvzp/v1 | https://www.protocols.io/view/crispr-nuclease-crisprn-genome-editing-c4w5yxg6 | Leonardo A Parra-Rivas | TITLE: CRISPR nuclease (CRISPRn) genome editing
AUTHORS: Leonardo A Parra-Rivas
[DESCRIPTION]
CRISPR nuclease (CRISPRn) genome editing
[STEPS]
1.
LentiCRISPRv2 plasmid (RRID:Addgene_52961) was used for α-syn genome editing. All sgRNAs
were designed using CRISPick (https://portals.broadinstitute.org/gppx/crispick/... | ["LentiCRISPRv2 plasmid (RRID:Addgene_52961) was used for α-syn genome editing. All sgRNAs\nwere designed using CRISPick (https://portals.broadinstitute.org/gppx/crispick/public) and examined for genome-wide sequence specificityusing the National Center for Biotechnology Information’s (NCBI) Basic Local Alignment Searc... |
28,086 | Ebola virus sequencing protocol | null | dx.doi.org/10.17504/protocols.io.7nwhmfe | null | Josh Quick | TITLE: Ebola virus sequencing protocol
AUTHORS: Josh Quick
[STEPS]
?. [cDNA preparation]
Mix the following components in an 0.2mL 8-strip tube;Component Volume50µM random hexamers 10mM dNTPs mix (10mM each) Template RNA Total
1... | ["[cDNA preparation]\nMix the following components in an 0.2mL 8-strip tube;Component Volume50µM random hexamers 10mM dNTPs mix (10mM each) Template RNA Total\n1 µl\n1 µl\n10 µl\n12 µl\nViral RNA input from a clinical sample sho... |
null | null | null | dx.doi.org/10.17504/protocols.io.e88bhzw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is part of the FOCUS™ Mitochondria Kit <a href="https://www.protocols.io/view/Collection-of-FOCUS-Mitochondria-Kit-protocols-e8tbhwn" target="_blank">collection</a>. Please refer to the appropriate protocol depending on your application.</p>
[BEFORE_START]
<p>A... | [] |
71,474 | PCR normalization and size selection with magnetic beads | 4 | dx.doi.org/10.17504/protocols.io.q26g7y859gwz/v2 | https://www.protocols.io/view/pcr-normalization-and-size-selection-with-magnetic-ch2st8ee | Dominik Buchner | TITLE: PCR normalization and size selection with magnetic beads
AUTHORS: Dominik Buchner
[DESCRIPTION]
This protocol describes how to clean up and normalize PCR products or DNA extracts and perform a size selection with carboxylated-magnetic beads and a PEG-NaCl buffer. It works by diluting the beads so that the bindi... | ["Shake the normalization solution until the beads are homogeneously resuspended", "Add 31 µL and 28 µL to a 250 µL U-bottom assay plate", "Add 9 µL", "To bind the DNA to the beads shake at", "Place the plate on a magnet to pellet the beads for 2 min", "Discard the supernatant by pipetting", "With the plate still on ... |
43,233 | Examination of the regression model to quantify the degree of low back pain and lower limb symptoms in patients with lumbar disc herniation by the Japanese Orthopaedic Association Back Pain Evaluation Questionnaire (JOABPEQ) | 1 | dx.doi.org/10.17504/protocols.io.bnf9mbr6 | https://www.protocols.io/view/examination-of-the-regression-model-to-quantify-th-bnf9mbr6 | Hayato Ishitani, Toshiyo Tamura, Shigehiko Kanaya | TITLE: Examination of the regression model to quantify the degree of low back pain and lower limb symptoms in patients with lumbar disc herniation by the Japanese Orthopaedic Association Back Pain Evaluation Questionnaire (JOABPEQ)
AUTHORS: Hayato Ishitani, Toshiyo Tamura, Shigehiko Kanaya
[DESCRIPTION]
<div class = "... | [] |
41,627 | Mirimus COVID-19 Pool Surveillance RT-PCR Testing | 4 | dx.doi.org/10.17504/protocols.io.bkv3kw8n | https://www.protocols.io/view/mirimus-covid-19-pool-surveillance-rt-pcr-testing-bkv3kw8n | Prem Premsrirut, Ana Vasileva, Huiting Cheng | TITLE: Mirimus COVID-19 Pool Surveillance RT-PCR Testing
AUTHORS: Prem Premsrirut, Ana Vasileva, Huiting Cheng
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Overview</span></div><div class = "text-block">At the start of the Pandemic in the US, New York was hit wit... | ["[Sample Pooling]\nPlace 24 tubes on rack. Place pool tube in position F8. Place organization tube in position F1. Barcode scan the rack. Initiate automated decapping on the Hamilton.", "[Sample Pooling]\nInitiate automated decapping. Move decapped rack to the Integra assist.", "[Sample Pooling]\nPlace 8 tubes of 400... |
null | null | null | dx.doi.org/10.17504/protocols.io.dq95z5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Several methods have been presented by Adams (1959) to determine adsorption kinetics of bacteriophages. One way to measure the adsorption efficiency of cyanophages is to assay for free unadsorbed phages (Suttle and Chan 1993). The principle of this assay is to add a known quanti... | [] |
44,757 | PBMC- 04 - In vitro Culture of TEFF+TREG - Proliferation of TEFF | 4 | dx.doi.org/10.17504/protocols.io.bpxvmpn6 | https://www.protocols.io/view/pbmc-04-in-vitro-culture-of-teff-treg-proliferatio-bpxvmpn6 | Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino | TITLE: PBMC- 04 - In vitro Culture of TEFF+TREG - Proliferation of TEFF
AUTHORS: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">List of published work using this procedure:</div><d... | ["Isolate TEFF and TREG with Miltenyi Kit according to the protocol PBMC- 03.\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 }", "Count both TEFF and TREG following the appropriate protocol (CELL COUNT- 02, or... |
22,294 | Centrifuge the whole blood to separate red blood cells | null | dx.doi.org/10.17504/protocols.io.zzwf77e | null | George Lykotrafitis | TITLE: Centrifuge the whole blood to separate red blood cells
AUTHORS: George Lykotrafitis
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Centrifuge the whole blood in order to obtain the red blood cells.</div></div>
[STEPS]
?. Centrifuge the whole blood using the parameters: 500 ×g, 4 ℃, and 5 m... | ["Centrifuge the whole blood using the parameters: 500 ×g, 4 ℃, and 5 min.", "Remove the plasma and buffy coat.", "Add the same volume of Alsever's solution as the remaining blood components.", "Centrifuge again using the parameters: 500 ×g, 4 ℃, and 5 min.", "Remove the top layer.", "Add the same volume of Alsever's... |
41,404 | eee 1 | 1 | null | https://www.protocols.io/view/eee-1-bkn4kvgw | Andrey A | TITLE: eee 1
AUTHORS: Andrey A
[STEPS]
?. asdasdasdad
?. asd
?. [asd] | ["asdasdasdad", "asd", "[asd]"] |
60,819 | aa-Onepot-seq | 4 | null | https://www.protocols.io/view/aa-onepot-seq-b7mtrk6n | Dongju Shin, JungWon Choi, Ji Hyun Lee, Duhee Bang | TITLE: aa-Onepot-seq
AUTHORS: Dongju Shin, JungWon Choi, Ji Hyun Lee, Duhee Bang
[DESCRIPTION]
aa-Onepot-seq follows protocol below:
Cells and beads preparation and incubation
Transfer and Scatter Cell-bead complexes
Cell lysis and beads isolation
cDNA synthesis
cDNA library amplification
NGS library preparation
... | ["[Cells and beads preparation and incubation] Prepare 1X106 cells to be stained", "[Cells and beads preparation and incubation] Add 100 µL of staining buffer to cell pellet and incubate for 5 minat 4 °C", "[Cells and beads preparation and incubation] Add 2 µLADT Antibody and incubate for 30 min at 4 °C", "[Cells and... |
65,909 | RNAi Mechanism using siRNA | 6 | null | https://www.protocols.io/view/rnai-mechanism-using-sirna-cckvsuw6 | BOC Sciences | TITLE: RNAi Mechanism using siRNA
AUTHORS: BOC Sciences
[DESCRIPTION]
RNA interference (RNAi) is a biological process in which RNA molecules silence specific genes, it's first discovered in plants and Caenorhabditis elegans and later in mammalian cells. This discovery is one of the most important advances in bio... | [] |
79,254 | B-PER Lysis--CHEM 384 | 4 | dx.doi.org/10.17504/protocols.io.261ge31jdl47/v1 | https://www.protocols.io/view/b-per-lysis-chem-384-crmwv47e | Ken Christensen | TITLE: B-PER Lysis--CHEM 384
AUTHORS: Ken Christensen
[DESCRIPTION]
The Thermo Scientific B-PER Bacterial Protein Extraction Reagent enables mild extraction of proteins from bacteria (E. coli) without the need for mechanical disruption. The reagent may be used for soluble protein extraction and inclusion body purific... | ["[B-PER Lysis to extract soluble protein] Pellet bacterial cells by centrifugation at 5000 × g in a tared tube for 10 min.", "[B-PER Lysis to extract soluble protein] Optional: Add 2 µLof lysozyme and 2 µL of DNase I per 1 mL of B-PER Reagent added.", "[B-PER Lysis to extract soluble protein] Add 4 mL of B-PER Reagent... |
86,652 | STREAM Benthic Metabarcoding Lab Protocol Draft | 1 | dx.doi.org/10.17504/protocols.io.5jyl8ppb6g2w/v1 | https://www.protocols.io/view/stream-benthic-metabarcoding-lab-protocol-draft-cyu4xwyw | Carley Maitland, Michael Wright, Mehrdad Hajibabaei | TITLE: STREAM Benthic Metabarcoding Lab Protocol Draft
AUTHORS: Carley Maitland, Michael Wright, Mehrdad Hajibabaei
[DESCRIPTION]
STREAM (Sequencing the Rivers for Environmental Assessment and Monitoring; www.stream-dna.org) is a Canada-wide community-based science program established in 2018 which is led by the rese... | ["[Homogenizing] Blenders should be decontaminated ahead of homogenization. Clean by fully disassembling blender components and rinsing with water. Visually inspect to ensure all debris has been removed before scrubbing all surfaces with ELIMINase ™ and rinsing with deionized (DI) water. Treat with UV light for 30 min ... |
46,219 | Nextera XT at 0.2X On the Mantis | 1 | dx.doi.org/10.17504/protocols.io.brdjm24n | https://www.protocols.io/view/nextera-xt-at-0-2x-on-the-mantis-brdjm24n | Allen Institute for Brain Science | TITLE: Nextera XT at 0.2X On the Mantis
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol to generate Nextera libraries using 0.2x reagents in a 96-well PCR plate using the Formulatrix Mantis instrument.</div><div class = "text-block"><span style = "... | [] |
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