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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23,000 | n-PCR for 10 samples | null | dx.doi.org/10.17504/protocols.io.2pygdpw | null | Matias Ruggieri, Carolina Berini, Nicolas Ducasa, Miroslav Malkovsky, Paul Fisch, Mirna Biglione | TITLE: n-PCR for 10 samples
AUTHORS: Matias Ruggieri, Carolina Berini, Nicolas Ducasa, Miroslav Malkovsky, Paul Fisch, Mirna Biglione
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">HTLV-1 diagnosis using PCR is based on the amplification of the viral DNA sequences. This is usually conducted using a... | ["Equipment and MaterialsPipettes10µl presterilized filter tips20µl presterilized filter tips200µl presterilized filter tips1000µl presterilized filter tipsThermal Cycle (we used TProfessional TRIO)Electrophoresis equipment", "Reagents and ChemicalsTaq DNA Polymerase kit (1000 U), by Qiagen, Catalog #: Cat No./ID: 2012... |
75,651 | eDNA extraction from MCE filter and Sterivex cartridge - LGC PUC Minas | 4 | dx.doi.org/10.17504/protocols.io.14egn2m9zg5d/v1 | https://www.protocols.io/view/edna-extraction-from-mce-filter-and-sterivex-cartr-cm5bu82n | Gabriel Antônio Mendes, Guilherme Costa Berger, Izabela Santos Mendes, Heron O Hilário, Daniel Cardoso de Carvalho | TITLE: eDNA extraction from MCE filter and Sterivex cartridge - LGC PUC Minas
AUTHORS: Gabriel Antônio Mendes, Guilherme Costa Berger, Izabela Santos Mendes, Heron O Hilário, Daniel Cardoso de Carvalho
[DESCRIPTION]
The following protocol covers the steps for extracting environmental DNA from MCE and Sterivex filters... | ["[Extração de eDNA de Sterivex] Após a limpeza da bancada e dos equipamentos, separar uma pinça para cada amostra (1 para cada filtro) e os cabos de bisturi. Colocá-los na solução de Hipoclorito de Sódio 25% durante 10 minutos. Após esse tempo, imergi-los na água destilada e, em seguida, borrifar álcool 70%. Após o ál... |
27,300 | Spectrophotometry method for the detection of Biochemical parameters | null | dx.doi.org/10.17504/protocols.io.6wchfaw | null | Xiaohua Du, Xia Liu, Mawolo James Blackar, Yingjie Zhou, Haifeng Wang, Fayang Liu, Zhiqing He | TITLE: Spectrophotometry method for the detection of Biochemical parameters
AUTHORS: Xiaohua Du, Xia Liu, Mawolo James Blackar, Yingjie Zhou, Haifeng Wang, Fayang Liu, Zhiqing He
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Definition of key terms</span></div><di... | ["[PART I: Sample preparation]\nTurn on the automatic analyser: Turn the automatic analyser on to warm up to give an accurate reading.While the automatic analyser was warming up, prepare the samples to be run.\nThe warm up process will take before the samples can be run.", "[PART I: Sample preparation]\nLoad the prop... |
96,446 | Exp_01 | 0 | dx.doi.org/10.17504/protocols.io.x54v9p91zg3e/v1 | https://www.protocols.io/view/exp-01-dae62bhe | José Eduardo De la Cruz Luna | TITLE: Exp_01
AUTHORS: José Eduardo De la Cruz Luna
[DESCRIPTION]
Creacion del primer experimento
[STEPS]
SECTION: Exp_01
1. Conectar los arduinos, resistencas y sensores(DS18B20) al protoboard
SECTION: Exp_01
2. Prepara el codigo que pueda capturar los datos del agua con los sensores
SECTION: Exp_01
3. Hervir el agu... | ["[Exp_01] Conectar los arduinos, resistencas y sensores(DS18B20) al protoboard", "[Exp_01] Prepara el codigo que pueda capturar los datos del agua con los sensores", "[Exp_01] Hervir el agua a 100ºC", "[Exp_01] Colocar un sensor en el asa y el otro dentro de la taza", "[Exp_01] Vertit el agua hirviendo a la taza", "[E... |
80,886 | Promega Wizard DNA extraction - Drosophila whole body protocol | 4 | null | https://www.protocols.io/view/promega-wizard-dna-extraction-drosophila-whole-bod-cs8wwhxe | finley.thomas. | TITLE: Promega Wizard DNA extraction - Drosophila whole body protocol
AUTHORS: finley.thomas.
[DESCRIPTION]
Edited version of the 'Promega Wizard Genomic DNA Purification' protocol optimised to work on pooled whole-body fruit fly samples.
[STEPS]
SECTION: Lysis & Incubation
1. Add 10 flies into a 1.5ml Eppen... | ["[Lysis & Incubation] Add 10 flies into a 1.5ml Eppendorf tube and cover with 300 µL .", "[Lysis & Incubation] Once the flies are throughly homogenised, add another 300 µL . \n\nBy this point, the solution should be opaque and red-brown in colour.", "[Lysis & Incubation] Use a micro-tube pestle to crush t... |
61,623 | In Vivo GCase Activity Assay | 4 | dx.doi.org/10.17504/protocols.io.eq2lyn8mqvx9/v1 | https://www.protocols.io/view/in-vivo-gcase-activity-assay-b8exrtfn | Laura Smith, Matthew Gegg | TITLE: In Vivo GCase Activity Assay
AUTHORS: Laura Smith, Matthew Gegg
[DESCRIPTION]
Assay uses the substrate PFB-FDGluc (5-(Pentafluorobenzoylamino)Fluorescein Di-β-D-Glucopyranoside)from ThermoScientific (Cat# P11947). Substrate is supposed to be taken up by late endosomes and lysosomes only and fluoresces green w... | ["[Measurement of GCase activity in lysosomes in live cells] Assay uses the substrate PFB-FDGluc (5-(Pentafluorobenzoylamino)Fluorescein Di-β-D-Glucopyranoside)from ThermoScientific (Cat# P11947). Substrate is supposed to be taken up by late endosomes and lysosomes only and fluoresces green when cleaved by lysosomal GC... |
43,634 | Fungal Extraction from Beetles | 3 | dx.doi.org/10.17504/protocols.io.bnusmewe | https://www.protocols.io/view/fungal-extraction-from-beetles-bnusmewe | You Li, Jiri Hulcr | TITLE: Fungal Extraction from Beetles
AUTHORS: You Li, Jiri Hulcr
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to extract fungal symbionts from beetles. </div><div class = "text-block"><span>This protocol is part of the Bark Beetle Mycobiome (BBM) Research Coordination... | [] |
58,238 | Collection of human vagal tissue samples for TEM imaging | 1 | dx.doi.org/10.17504/protocols.io.b446qyze | https://www.protocols.io/view/collection-of-human-vagal-tissue-samples-for-tem-i-b446qyze | Terry Powley, Deborah Jaffey, Anita Gupta, Plamen Mihaylov, John Wo | TITLE: Collection of human vagal tissue samples for TEM imaging
AUTHORS: Terry Powley, Deborah Jaffey, Anita Gupta, Plamen Mihaylov, John Wo
[DESCRIPTION]
This protocol describes the methods used to generate samples of human vagus tissue suitable for TEM imaging.
[BEFORE_START]
Ensure that all appropriate authoriza... | ["[Sampling] Vagus nerve samples were obtained intra-operatively from organ donors. Separate consents for organ donation and research were obtained. Informed consent for study participation was obtained from a parent and/or legal guardian. No organ donors were prisoners. A diagnosis of brain death or circulatory death ... |
51,337 | PBMC 10X Genomics Single Cell CUT&Tag Protocol | 1 | dx.doi.org/10.17504/protocols.io.bwdhpa36 | https://www.protocols.io/view/pbmc-10x-genomics-single-cell-cut-amp-tag-protocol-bwdhpa36 | Anca B. Mihalas, Hatice S. Kaya-Okur, Steven Henikoff, Anoop P. Patel | TITLE: PBMC 10X Genomics Single Cell CUT&Tag Protocol
AUTHORS: Anca B. Mihalas, Hatice S. Kaya-Okur, Steven Henikoff, Anoop P. Patel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is based on the bulk CUT&Tag protocol developed in the Henikoff laboratory (</span><a href="https:/... | ["[A. Nuclei isolation protocol]\nNOTES:1. All samples and reagents are kept on ice (wet ice) or at 4°C.2. Use low retention tubes (Thermo Scientific # 3451) and pipette tips (Corning # 4140, 4138, 4136), and avoid over pipetting throughout the entire protocol.3. All spins are at 500 RCF for 5 minutes at 4°C, using a s... |
91,094 | Alfaxalone is an Effective Anesthetic for the Electrophysiological Study of Anoxia-Tolerance Mechanisms in Western Painted Turtle Pyramidal Neurons | 1 | dx.doi.org/10.17504/protocols.io.x54v9pzjzg3e/v1 | https://www.protocols.io/view/alfaxalone-is-an-effective-anesthetic-for-the-elec-c47wyzpe | Haushe Suganthan, Domenic Di Stefano, Leslie Buck | TITLE: Alfaxalone is an Effective Anesthetic for the Electrophysiological Study of Anoxia-Tolerance Mechanisms in Western Painted Turtle Pyramidal Neurons
AUTHORS: Haushe Suganthan, Domenic Di Stefano, Leslie Buck
[DESCRIPTION]
Many anesthetics have long-term effects on ion channels and are not appropriate for same ... | ["[Animal Care and Cortical Sheet Preparation] Obtain the adult turtles (Chrysemys picta bellii) from Niles Biological and are then housed in a large aquarium equipped with a freshwater recirculating filter system set at 20 °C, a non-aquatic basking platform, and a heat lamp.", "[Animal Care and Cortical Sheet Preparat... |
93,229 | snPATHO-seq | 4 | dx.doi.org/10.17504/protocols.io.8epv5x58dg1b/v1 | https://www.protocols.io/view/snpatho-seq-c7amzic6 | Tony Wang, Michael Roach, Jasmine Plummer, Luciano G Martelotto | TITLE: snPATHO-seq
AUTHORS: Tony Wang, Michael Roach, Jasmine Plummer, Luciano G Martelotto
[DESCRIPTION]
Formalin-fixed paraffin-embedded (FFPE) samples are valuable but under-utilised in single-cell omics research due to their low DNA and RNA quality. Leveraging recent single-cell genomic technology advances, we int... | ["[Paraffin removal] Cut 1 or 2 approximately 25 μm-thick sections (punches are also possible) and transfer to a 1.5 mL Eppendorf tube.", "[Paraffin removal] Add 1 mL and incubate for 10 min at Room temperature or 50-55 °C", "[Rehydration] Add 1 mL and incubate for 1 min at Room temperature, then carefully remove ethan... |
96,069 | Creating a Manual Consensus Sequence from FASTQ with UGENE | 0 | null | https://www.protocols.io/view/creating-a-manual-consensus-sequence-from-fastq-wi-c93dz8i6 | Stephen Douglas Russell | TITLE: Creating a Manual Consensus Sequence from FASTQ with UGENE
AUTHORS: Stephen Douglas Russell
[DESCRIPTION]
Current versions of automated nanopore amplicon pipelines sometimes (rarely) produce erroneous consensus sequences based on low quality reads that are being incorporated into the final result. It is sometim... | ["[Install Software, Retrieve Data, Import to UGENE] Download and install the latest version of UGENE at https://ugene.net/.", "[Install Software, Retrieve Data, Import to UGENE] Retrieve the FASTQ file of your sequence. If you are using MycoMap, first go to your MycoMap sequence accession. The easiest way to find it i... |
null | null | null | dx.doi.org/10.17504/protocols.io.nrrdd56 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Table 1: Age distribution of subjects staged for AMD</p>
<p>Table 2: CFI levels in subjects with AMD</p>
<p>Fig. 3: Preincubation of CFI with amyloid B (1-42) reduces CFI bioactivity</p>
<p>Fig. 4: Anti-amyloid B antibody, GSK933776 effectively blocks amyloid B's ability to i... | [] |
43,715 | Identifying and Validating Tankyrase Binders and Substrates: A Candidate Approach | 2 | dx.doi.org/10.17504/protocols.io.bnxbmfin | https://www.protocols.io/view/identifying-and-validating-tankyrase-binders-and-s-bnxbmfin | Katie Pollock, Michael Ranes, Ian Collins, Sebastian Guettler | TITLE: Identifying and Validating Tankyrase Binders and Substrates: A Candidate Approach
AUTHORS: Katie Pollock, Michael Ranes, Ian Collins, Sebastian Guettler
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The poly(ADP-ribose)polymerase (PARP) enzyme tankyrase (TNKS/ARTD5, TNKS2/ARTD6) uses... | [] |
46,759 | Left Ventricle Contraction Curves | 5 | dx.doi.org/10.17504/protocols.io.brwfm7bn | https://www.protocols.io/view/left-ventricle-contraction-curves-brwfm7bn | Giorgio Bozzi | TITLE: Left Ventricle Contraction Curves
AUTHORS: Giorgio Bozzi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The folder LVOBJEVL.zip contains the LeftVentricle.exe file and the KLVG directory with service files. Unzip the folder.</div><div class = "text-block">LeftVentricle.exe Program</div><div ... | ["This Zip LVOBJEVL contains LeftVentricle.exe and a service DIR KLVG."] |
70,952 | Splenocyte isolation from mice | 4 | null | https://www.protocols.io/view/splenocyte-isolation-from-mice-chigt4bw | sffschn | TITLE: Splenocyte isolation from mice
AUTHORS: sffschn
[DESCRIPTION]
Simple protocol for isolation of spleenocytes from mouse spleen.
[STEPS]
1. Collect spleens in some PBS
2. Place spleen on a 70 µm mesh filter ontop of a 50 mL Falcon
2.1. max. 2 spleens per filter
3. pass through 70 µm mesh filter using a pis... | ["Collect spleens in some PBS", "Place spleen on a 70 µm mesh filter ontop of a 50 mL Falcon", "max. 2 spleens per filter", "pass through 70 µm mesh filter using a pistol of a 2 mL syringe", "wash with FACS buffer and top up to 50 mL \n50 mL \n \n 2 %\n 1 mM", "Spin down for 5 min \n400 x g, 5 min, 4 °C", "Pour of... |
82,298 | Uncovering the Citation Landscape: Exploring OpenCitations COCI, OpenCitations Meta, and ERIH-PLUS in Social Sciences and Humanities Journals - Workflow | 5 | dx.doi.org/10.17504/protocols.io.n92ldpeenl5b/v3 | https://www.protocols.click/view/uncovering-the-citation-landscape-exploring-openci-cuk2wuye | Marta Soricetti, Sara Vellone, Olga Pagnotta, Lorenzo Paolini | TITLE: Uncovering the Citation Landscape: Exploring OpenCitations COCI, OpenCitations Meta, and ERIH-PLUS in Social Sciences and Humanities Journals - Workflow
AUTHORS: Marta Soricetti, Sara Vellone, Olga Pagnotta, Lorenzo Paolini
[DESCRIPTION]
Purpose
The main purpose of this research is to answer to three different... | ["[Processing of Input Data] We tried to define a mapping of the datasets to understand what are the information that the three datasets have in common. By looking at the data and the columns' names, we have identified the following:\n \nTaking as a starting point META, we have identified the COCI columns \"citing\" an... |
74,745 | Potential determinants of COVID-19 vaccine confidence and receptivity among the primary school’s stakeholders in Bangladesh: A cross-sectional study to assess the effects of education | 1 | dx.doi.org/10.17504/protocols.io.ewov1o2b2lr2/v1 | https://www.protocols.io/view/potential-determinants-of-covid-19-vaccine-confide-ck8zuzx6 | dn.roy | TITLE: Potential determinants of COVID-19 vaccine confidence and receptivity among the primary school’s stakeholders in Bangladesh: A cross-sectional study to assess the effects of education
AUTHORS: dn.roy
[DESCRIPTION]
This method designed to (i) investigate COVID-19 vaccine confidence and receptivity among the prim... | [] |
95,107 | Measuring dopamine release in human-derived iPSCs using High-Performance Liquid Chromatography (HPLC) coupled to Electrochemical Detection (ECD) | 1 | dx.doi.org/10.17504/protocols.io.q26g7p2bkgwz/v1 | https://www.protocols.io/view/measuring-dopamine-release-in-human-derived-ipscs-c85bzy2n | Kaitlyn ML Cramb, Stephanie J Cragg, Richard Wade-Martins | TITLE: Measuring dopamine release in human-derived iPSCs using High-Performance Liquid Chromatography (HPLC) coupled to Electrochemical Detection (ECD)
AUTHORS: Kaitlyn ML Cramb, Stephanie J Cragg, Richard Wade-Martins
[DESCRIPTION]
This protocol allows for the detection of evoked or tonic dopamine release from human ... | ["[Preparation] Add 1 µL of perchloric acid (PCA) to a labelled light-protected 1.5 mL Eppendorf tube for each sample.", "[Preparation] Prepare Ringers Buffers for tonic or evoked release (see Materials). Store short-term at 4°C.", "[Dopamine (DA) Release Assay] Aspirate media from hiPSC-DANs plated as stated in guidel... |
85,848 | Indirect Proximity Ligation Assay (PLA) - Brightfield | 1 | dx.doi.org/10.17504/protocols.io.bp2l6x94klqe/v1 | https://www.protocols.io/view/indirect-proximity-ligation-assay-pla-brightfield-cx3yxqpw | Ayse Ulusoy, Rita Pinto-Costa, Angela Rollar, Donato Di Monte | TITLE: Indirect Proximity Ligation Assay (PLA) - Brightfield
AUTHORS: Ayse Ulusoy, Rita Pinto-Costa, Angela Rollar, Donato Di Monte
[DESCRIPTION]
Indirect Proximity Ligation Assay (PLA) is a powerful molecular technique used to detect and visualize protein-protein interactions, protein modifications, and protein compl... | ["[Day 1] Pick 35um cut brain sections and transfer them to 1.5 mL Eppendorf tubes\nNote: all incubation and wash steps are performed by shaking Eppendorf tubes at 250rpm (e.g., thermomixer)", "[Day 1] Wash 2x5 min with Tris-HCl", "[Day 1] Peroxidase quenching with BloxAll solution\n\nuse 300 µLand incubate for 30min",... |
null | null | null | dx.doi.org/10.17504/protocols.io.j7ecrje | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This extraction protocol follows the DArT DNA Extraction protocol but contains modifications (including increasing the concentration of PVP to 4 %</p>
[STEPS]
?.
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... | [] |
86,558 | NCBI submission protocol for microbial pathogen surveillance | 1 | dx.doi.org/10.17504/protocols.io.4r3l284pql1y/v9 | https://www.protocols.io/view/ncbi-submission-protocol-for-microbial-pathogen-su-cyr6xv9e | 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 t... | ["[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... |
63,708 | Administrative Carlos Virella | 5 | dx.doi.org/10.17504/protocols.io.kxygxz22ov8j/v1 | https://www.protocols.io/view/administrative-carlos-virella-caf4sbqw | Carlos Virella | TITLE: Administrative Carlos Virella
AUTHORS: Carlos Virella
[DESCRIPTION]
A set of strings dedicated for the administration of the Carlos
[STEPS]
1. 233c8ea3000000000000000000000000000000000000000000000000000000000000012000000000000000000000000000000000000000000000000000000000000001c0000000000000000000000000000000... | ["233c8ea3000000000000000000000000000000000000000000000000000000000000012000000000000000000000000000000000000000000000000000000000000001c0000000000000000000000000000000000000000000000000000000000000022000000000000000000000000000000000000000000000000000000000000002a0000000000000000000000000000000000000000000000000000000... |
80,235 | RCA-NGS for RNA viruses with ONT V14 chemistry | 4 | dx.doi.org/10.17504/protocols.io.n92ldpx89l5b/v1 | https://www.protocols.io/view/rca-ngs-for-rna-viruses-with-ont-v14-chemistry-cskjwcun | Masayasu Misu, Tomoki Yoshikawa, Satoko Sugimoto, Yuki Takamatsu, Takeshi Kurosu, Yukiteru Ouji, Masahide Yoshikawa, Masayuki Shimojima, Hideki Ebihara, Masayuki Saijo | TITLE: RCA-NGS for RNA viruses with ONT V14 chemistry
AUTHORS: Masayasu Misu, Tomoki Yoshikawa, Satoko Sugimoto, Yuki Takamatsu, Takeshi Kurosu, Yukiteru Ouji, Masahide Yoshikawa, Masayuki Shimojima, Hideki Ebihara, Masayuki Saijo
[DESCRIPTION]
Note that this version of the protocl was adopted to V14 chemistry of ONT.... | ["[Preparation for virus supernatant] Centrifuge the working stock virus to remove debris.\n 6000 x g, 10 min", "[Preparation for virus supernatant] Unwanted DNA and RNA mainly originating from the virus-infected cells are digested using .", "[The viral genomic RNA extraction] The viral genomic RNA extraction is perfo... |
42,609 | FISH and antibody staining | 4 | null | https://www.protocols.io/view/fish-and-antibody-staining-bmurk6v6 | 张 雪 | TITLE: FISH and antibody staining
AUTHORS: 张 雪
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">荧光原位杂交方法与一般原位杂交方法类似，只是为了不影响后续抗体显色，第一天所用的杂交温度较低，可选择55-65°C，还有第二天加入的是anti-dig-POD（4°C冰箱自取）而不是anti-dig-AP（领抗体），最后显色方法也有不同。</div></div>
[STEPS]
?. [Day1]
复水：75%MetOH+25%PBT 1ml shake for 5min
?. [Day1]
50%Met... | ["[Day1]\n复水：75%MetOH+25%PBT 1ml shake for 5min", "[Day1]\n50%MetOH+50%PBT 5min", "[Day1]\n25%MetOH+75%PBT 5min", "[Day1]\n100%PBT 5min 1/4\n融化PK", "[Day1]\n100%PBT 5min 2/4", "[Day1]\n100%PBT 5min 3/4", "[Day1]\n100%PBT 5min 4/4", "[Day1]\n透化：Proteinase K: PBT = 1 : 2000 (终浓度5µg/ml），5min", "[Day1]\n再固定：4%PFA 20min\n加P... |
94,040 | Processing frozen human blood samples for population-scale SQK-LSK114 Oxford Nanopore long-read DNA sequencing SOP V2 | 1 | dx.doi.org/10.17504/protocols.io.5qpvo3639v4o/v1 | https://www.protocols.io/view/processing-frozen-human-blood-samples-for-populati-c73yzqpw | Abigail Miano-Burkhardt, Pilar Alvarez Jerez, Laksh Malik, Cornelis Blauwendraat, Kimberley J Billingsley, on behalf of the CARD Long-read Team | TITLE: Processing frozen human blood samples for population-scale SQK-LSK114 Oxford Nanopore long-read DNA sequencing SOP V2
AUTHORS: Abigail Miano-Burkhardt, Pilar Alvarez Jerez, Laksh Malik, Cornelis Blauwendraat, Kimberley J Billingsley, on behalf of the CARD Long-read Team
[DESCRIPTION]
Abstract:
As part of the GP... | ["Part 1: Preparing Blood Samples (~30 min for 24 samples)", "Obtain blood samples from -80C freezer and thaw in water bath at 37 °C for 15 min\n\nNote: This is specifically for 6mL tubes, if starting with only 1mL thaw until warm (~ 5 min)", "Inversion mix blood 10x immediately before use. \n\nNote: The blood sample n... |
103,282 | qPCR based multipathogen detection for Salmonella Paratyphi "A" and Vibrio cholerae from wastewater samples | 0 | dx.doi.org/10.17504/protocols.io.6qpvr8m8plmk/v1 | https://www.protocols.io/view/qpcr-based-multipathogen-detection-for-salmonella-dg4s3ywe | Dilip Abraham, Blossom Benny Sam, Nirmal Kumar, Raju Ravi, Venkata Raghava Mohan | TITLE: qPCR based multipathogen detection for Salmonella Paratyphi "A" and Vibrio cholerae from wastewater samples
AUTHORS: Dilip Abraham, Blossom Benny Sam, Nirmal Kumar, Raju Ravi, Venkata Raghava Mohan
[DESCRIPTION]
The following protocol is optimized for the detection of Salmonella Paratyphi A and Vibrio ... | ["[Primer-Probe panel] PCR 2: Vibrio cholerae_1 PCR panel", "[Primer-Probe panel] PCR 3: Vibrio cholerae_2 PCR panel", "[Primer-probe reconstitution] Multiply nmol value by 10 to get the required volume of Nuclease Free Water (NFW) needed to reconstitute the lyophilized primer/probes.\nEx: For a primer with 30 nmoles, ... |
19,529 | Genotyping chip data lift-over to reference genome build GRCh38/hg38 | null | dx.doi.org/10.17504/protocols.io.xbhfij6 | null | Kalle Pärn, Javier Nunez Fontarnau, Marita A. Isokallio, Timo Sipilä, Elina Kilpelainen, Aarno Palotie, Samuli Ripatti, Priit Palta | TITLE: Genotyping chip data lift-over to reference genome build GRCh38/hg38
AUTHORS: Kalle Pärn, Javier Nunez Fontarnau, Marita A. Isokallio, Timo Sipilä, Elina Kilpelainen, Aarno Palotie, Samuli Ripatti, Priit Palta
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Genome build lift-over]
If the genotyping... | ["[Genome build lift-over]\nIf the genotyping chip used an older reference genome version (e.g. GRCh37/hg19) and is in PLINK format, the data have to be lifted over to human genome build version 38 (GRCh38/hg38).For the genome build lift-over we suggest Will Rayner's method.Download your genotyping chip specific build ... |
50,003 | Efficacy and safety of endovascular arteriovenous fistula creation with comparison to surgically created fistulas: a systematic review and meta-analysis protocol | 1 | dx.doi.org/10.17504/protocols.io.bu3tnynn | https://www.protocols.io/view/efficacy-and-safety-of-endovascular-arteriovenous-bu3tnynn | Yoshinosuke Shimamura, Yasutaka Kuniyoshi, Hajime Yamazaki, Yasushi Tsujimoto | TITLE: Efficacy and safety of endovascular arteriovenous fistula creation with comparison to surgically created fistulas: a systematic review and meta-analysis protocol
AUTHORS: Yoshinosuke Shimamura, Yasutaka Kuniyoshi, Hajime Yamazaki, Yasushi Tsujimoto
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-blo... | ["[Introduction]\nFunctional vascular access is the lifeline of hemodialysis patients. The Kidney Disease Outcomes Quality Initiative guideline strongly recommends the creation of arteriovenous fistulas for long-term vascular access. Although arteriovenous fistulas have been created using open surgery, endovascular tec... |
null | null | null | dx.doi.org/10.17504/protocols.io.iuzcex6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a protocol for carrying out RNA Stable Isotope Probing experiments using seawater or vent fluids to examine microbial bicarbonate uptake. It was developed at Axial Seamount to examine autotrophy in deep-sea hydrothermal vent fluids. We have used modified versions in s... | [] |
104,429 | ForBio Course ONT Barcoding Protocol | 0 | null | https://www.protocols.io/view/forbio-course-ont-barcoding-protocol-dh8m39u6 | Emily Hartop | TITLE: ForBio Course ONT Barcoding Protocol
AUTHORS: Emily Hartop
[DESCRIPTION]
Protocols for ONT Barcoding Course at NTNU August 2024
[STEPS]
SECTION: HotSHOT Extraction
3. Pipette 10-20 μL of HOTSHOT alkaline lysis reagent into wells of a microplate
SECTION: HotSHOT Extraction
4. Remove specimens onto a clean pape... | ["[HotSHOT Extraction] Pipette 10-20 μL of HOTSHOT alkaline lysis reagent into wells of a microplate", "[HotSHOT Extraction] Remove specimens onto a clean paper towel, dab on towel before loading to remove excess ethanol", "[HotSHOT Extraction] Load specimens and check to make sure all specimens are submerged. If neces... |
54,022 | Microfluidics 5: PDMS Microchannel Bonding on Glass/PDMS | 1 | dx.doi.org/10.17504/protocols.io.byzepx3e | https://www.protocols.io/view/microfluidics-5-pdms-microchannel-bonding-on-glass-byzepx3e | Serhat Sevli, C. Yunus Sahan | TITLE: Microfluidics 5: PDMS Microchannel Bonding on Glass/PDMS
AUTHORS: Serhat Sevli, C. Yunus Sahan
[DESCRIPTION]
Microfluidic chips, made of PDMS, are one-side open when fabricated. Another layer of glass, PDMS, or etc is needed. Liquid seal is provided by complete covalent bonding between layers or by external fo... | ["[Oxygen Plasma Exposure] 1.0.1. Cured PDMS manufactured at previous steps using lithography or 3D printed molds are cut or removed from the mold and put inside a clean petri dish. Since PDMS is vulnerable to surface adsorption of dust, each must be clean and performed inside cleanroom facilities.\n\n1.0.2. NehirBT's ... |
36,946 | Single-step purification by heat shock | 1 | dx.doi.org/10.17504/protocols.io.bgbsjsne | https://www.protocols.io/view/single-step-purification-by-heat-shock-bgbsjsne | Hossein Tarrahimofrad, Amir Meimandipour, Sareh Arjmand, Mohammadtaghi Beigi Nassiri, Ehsan Jahangirian, Hossein Tavana, Javad Zamani, Somayyeh Rahimnahal, Saeed Aminzadeh | TITLE: Single-step purification by heat shock
AUTHORS: Hossein Tarrahimofrad, Amir Meimandipour, Sareh Arjmand, Mohammadtaghi Beigi Nassiri, Ehsan Jahangirian, Hossein Tavana, Javad Zamani, Somayyeh Rahimnahal, Saeed Aminzadeh
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>After the c... | ["Cultivation cells , collected by centrifugation and resuspended in 4 ml lysis buffer (, , and at )\n50 mL\n37 °C\nCentrifuge: 3500 34, 30 min, 4 10\n[NaH2PO4]\n[NaCl]\n[Imidazole]\n[Tween 20]", "The mixture was sonicated with 4 × pulses followed by rest between cycles at .\n[Amper 0.7]\n4 °C", "The crude e... |
89,682 | Cell Lysate Preparation & Immunoblotting Protocols | 4 | null | https://www.protocols.io/view/cell-lysate-preparation-amp-immunoblotting-protoco-c3tsynne | aasirvatham | TITLE: Cell Lysate Preparation & Immunoblotting Protocols
AUTHORS: aasirvatham
[DESCRIPTION]
The purpose of this experiment is to investigate the effects of forskolin-mediated cAMP activation on the viability of LPS-treated Schwann cells. The immortalized rat RT4-D6P2T cell line (ATCC #CRL-2768) was cultured and r... | ["[To prepare RT4-D6P2T cell lysates (for three 6-well plates):] Aseptically culture immortalized rat RT4-D6P2T Schwann cells (ATCC, Cat #CRL-2768, Manassas, VA) in Dulbecco’s Modified Eagle Medium (DMEM) (ATCC, Cat #30-2002, Manassas, VA) supplemented with 10% fetal bovine serum (FBS) (Thermo Fisher, Cat #16000044, Wa... |
50,683 | Dissociation of Jejunum cells for clumps sorting | 1 | dx.doi.org/10.17504/protocols.io.bvq3n5yn | https://www.protocols.io/view/dissociation-of-jejunum-cells-for-clumps-sorting-bvq3n5yn | Rita Manco, Inna Averbukh, Ziv Porat, Keren Bahar Halpern, Ido Amit, Shalev Itzkovitz | TITLE: Dissociation of Jejunum cells for clumps sorting
AUTHORS: Rita Manco, Inna Averbukh, Ziv Porat, Keren Bahar Halpern, Ido Amit, Shalev Itzkovitz
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Single-cell RNA sequencing combined with spatial information on landmark genes enables the reconstruc... | ["[Dissociation of Jejunum cells for clumps sorting]\nPrepare buffers:Buffer1 (25ml): DPBS (-/-) 24.5 mlEDTA 0.5M (10mM) 500 µlBuffer2 (50ml): For Hoechst DMEM high glucose 44.5 ml10% FBS 5 mlHepes 1M (10mM) 500 µl\nDPBS (-/-) 24.5 mlEDTA 0.5M (10mM) 500 µl\nDMEM high glucose 44.5 ml10% FBS 5 mlHepes 1M (10mM) 500 µl",... |
71,123 | Acetone extraction of bacteria pellet for HPLC (2022 iGEM) | 1 | dx.doi.org/10.17504/protocols.io.eq2ly7peelx9/v1 | https://www.protocols.io/view/acetone-extraction-of-bacteria-pellet-for-hplc-202-chptt5nn | Team Fudan iGEM | TITLE: Acetone extraction of bacteria pellet for HPLC (2022 iGEM)
AUTHORS: Team Fudan iGEM
[DESCRIPTION]
Pre-cold acetone is generally used for protein precipitation. Here, we collect the supernatant for membrane lipid analysis.
[STEPS]
2. Add 4 times the volume -20°C acetone (3 mL in our case) to the extract, and vo... | ["Add 4 times the volume -20°C acetone (3 mL in our case) to the extract, and vortex.", "Incubate sample at -20°C for 1 hour. 60 min", "Centrifuge at 13500 rpm for 10 minutes at 4°C. Collect the supernatant without touching the protein pellet.", "Store the acetone extracted sample at -80°C for long term use, or -20°C f... |
null | null | null | dx.doi.org/10.17504/protocols.io.ufaetie | null | null | TITLE: No Title
AUTHORS:
[STEPS]
SECTION: Procedure
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SECTION: ... | ["[Procedure] Aspirate Cell-Tak solution if not already done.", "[Procedure] Add 50 μl medium to wells A and H and 50 μl cells to wells B-G. Samples are generally run in duplicate or triplicate on each plate. Cell number is 1.5×10^5 cells per well.", "[Procedure] Place plate in the carrier and place in centrifuge. S... |
19,430 | Weekly Quality Control | null | dx.doi.org/10.17504/protocols.io.w8efhte | null | Lukas Snoek, Tinka Beemsterboer | TITLE: Weekly Quality Control
AUTHORS: Lukas Snoek, Tinka Beemsterboer
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The weekly quality control at the Spinoza Centre REC evaluates the signal quality/performance of the 3T Philips Achieva TX (R5, v3.0).</div></div>
[STEPS]
?. [PIQT (spatial stabili... | ["[PIQT (spatial stability)]\nRun PIQTDuration: 20 minutesThis scan evaluates several internal parameters of the scanner, including the stability of the gradient coils. This is done by scanning a phantom from which the specs are known.The protocol is as follows: Hook up the PIQT-headcoil (see picture below) aCheck whet... |
null | null | null | dx.doi.org/10.17504/protocols.io.dw97h5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<span class="cit-title">The following is a modification of a Scherz R., 2001 method for colony embedding. The protocol described here is from:<br /><br />Sarah Piccirillo, <em>et. al. </em><a href="http://www.genetics.org/content/184/3/707" target="_blank">The Rim101p/PacC Pathw... | [] |
9,248 | One-pot Optimization of Genetic Circuits using Poly-transfections | null | dx.doi.org/10.17504/protocols.io.k98cz9w | null | Jeremy Gam, Breanna DiAndreth, Jin Huh, Ross Jones, Ron Weiss | TITLE: One-pot Optimization of Genetic Circuits using Poly-transfections
AUTHORS: Jeremy Gam, Breanna DiAndreth, Jin Huh, Ross Jones, Ron Weiss
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. [Plasmid Design and Cloning]
Poly-transfections can be performed either with the transfection marker included on th... | ["[Plasmid Design and Cloning]\nPoly-transfections can be performed either with the transfection marker included on the same plasmid or by cotransfecting a different transfection marker plasmid with each different gene of interest. For co-transfections, skip to step 6 but remember to mix the transfection marker plasmid... |
38,342 | Nuclei Isolation from Human Frozen Liver | 1 | dx.doi.org/10.17504/protocols.io.bhpej5je | https://www.protocols.io/view/nuclei-isolation-from-human-frozen-liver-bhpej5je | Sanjay Subramanian, Stacey Huppert | TITLE: Nuclei Isolation from Human Frozen Liver
AUTHORS: Sanjay Subramanian, Stacey Huppert
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used to isolate human liver nuclei from frozen samples in an effort to facilitate human nuclei extraction for use in single nuclear RNA sequenc... | ["Thaw small tissue sample from frozen preservation medium at room temperature and wash in 1x PBS", "Briefly mince tissue into small chunks using a scalpel and/or razor in petri dish on ice", "Homogenize chunks using Tissue Grinder Dounce with Pestle A in 500μL to 1mL of ice-cold TST buffer\n[TST buffer]\n1mL Tissue Gr... |
63,404 | Изаберите Optimus Gel најбољих за бол у зглобовима по доброј цени! | 3 | dx.doi.org/10.17504/protocols.io.5jyl89kn7v2w/v1 | https://www.protocols.io/view/optimus-gel-b96kr9cw | Optimus Gel Iskustva | TITLE: Изаберите Optimus Gel најбољих за бол у зглобовима по доброј цени!
AUTHORS: Optimus Gel Iskustva
[DESCRIPTION]
Оптимус Гел је нови квалитетан производ који обједињује најновија научна достигнућа која заувек ублажавају и отклањају болове у зглобовима, костима и мишићима! Наручите данас са 50% попуста!
[STEPS] | [] |
45,961 | C-SOP-601: Operation of the Illumina MiSeq for Whole Genome Sequencing (WGS) | 4 | null | https://www.protocols.io/view/c-sop-601-operation-of-the-illumina-miseq-for-whol-bq5hmy36 | Mihir Kekre | TITLE: C-SOP-601: Operation of the Illumina MiSeq for Whole Genome Sequencing (WGS)
AUTHORS: Mihir Kekre
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The Illumina® MiSeq™ system combines proven sequencing by synthesis (SBS) technology with a revolutionary workflow that lets you go from DNA to ana... | ["[Before Starting]\nPrior to initiating the protocol, ensure that all active workbenches are cleaned with 80% ethanol, all relevant personal protective clothing is worn and the work area is prepared according to local GLP guidelines for molecular methods.Create an organised bench space by clearing away all clutter in ... |
34,550 | Blunt end ligation | null | dx.doi.org/10.17504/protocols.io.bdywi7xe | null | Keyong Sun | TITLE: Blunt end ligation
AUTHORS: Keyong Sun
[STEPS]
?. [Prepare DNA Fragment]
Amplify target DNA fragment using high-fidelity DNA polymerase for blunt end fragment
?. [Phosphorylation of Recovered DNA ]
?. [Prepare DNA Fragment]
Purify DNA using gel extraction
?. [Ligation]
?.
?.
?. | ["[Prepare DNA Fragment]\nAmplify target DNA fragment using high-fidelity DNA polymerase for blunt end fragment", "[Phosphorylation of Recovered DNA ]", "[Prepare DNA Fragment]\nPurify DNA using gel extraction", "[Ligation]"] |
null | null | null | dx.doi.org/10.17504/protocols.io.emgbc3w | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For use in <a href="https://www.protocols.io/view/Generating-viral-metagenomes-from-the-coral-holobi-ejgbcjw" target="_blank">Generating viral metagenomes from the coral holobiont</a>.
[STEPS]
?.
?.
?.
?. | [] |
79,063 | Compound Screening and Growth Curves | 1 | dx.doi.org/10.17504/protocols.io.6qpvr4qzzgmk/v2 | https://www.protocols.io/view/compound-screening-and-growth-curves-crfxv3pn | Carlos Carlos Goller | TITLE: Compound Screening and Growth Curves
AUTHORS: Carlos Carlos Goller
[DESCRIPTION]
Overview
The bacterial genus Delftia was named for the city of Delft in the Netherlands, where the species type was isolated and for the Delft research groups that had a critical role in the early development of bacteriology. Speci... | ["[Plate Setup and Incubation] Read the procedure listed below. Discuss with your lab partner the key steps to program the liquid handler to successfully complete this task. Pay attention to the reagents, tube format, and equipment we have. Remember the goal: reproducibly testing compounds (with replicates) and includi... |
null | null | null | dx.doi.org/10.17504/protocols.io.ebfbajn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol is part of the VERVE holiday drive to collect exotic off-the-shelf laboratory recipes. More details <a href="https://www.protocols.io/g/verve-net/news/call-for-recipes" target="_blank">here</a>.<br /><img id="s-mce-img" class="s-mce-img" src="https://s3.amazonaws.c... | [] |
56,724 | Preparing Gene of interest for GateWay cloning (2 step PCR process) | 1 | dx.doi.org/10.17504/protocols.io.b3muqk6w | https://www.protocols.io/view/preparing-gene-of-interest-for-gateway-cloning-2-s-b3muqk6w | Johannes Wolfram JWD Debler | TITLE: Preparing Gene of interest for GateWay cloning (2 step PCR process)
AUTHORS: Johannes Wolfram JWD Debler
[DESCRIPTION]
GateWay recombination cloning is achieved by flanking your gene of interest with GateWay attachment sites. In our case attB1 and attB2. Those sites are added to the PCR product via primers with... | ["[Primer design] There are a few things we need to keep in mind when designing the primers in the wider context of Gateway cloning. The idea is that you create an \"entry clone\" containing your gene of interest. Ususally INCLUDING the start codon, but EXCLUDING the stop codon. This is because one of the points of Gat... |
48,737 | Fully defined human pluripotent stem cell-derived microglia and tri-culture system model C3 production in Alzheimer’s disease | 1 | dx.doi.org/10.17504/protocols.io.btt9nnr6 | https://www.protocols.io/view/fully-defined-human-pluripotent-stem-cell-derived-btt9nnr6 | Sudha R. Guttikonda, Lisa Sikkema, Jason Tchieu, Nathalie Saurat, Ryan Walsh, Oliver Harschnitz, Gabriele Ciceri, Marjolein Sneeboer, Linas Mazutis, Manu Setty, Paul Zumbo, Doron Betel, Lot D. de Witte, Dana Pe'er, Lorenz Studer | TITLE: Fully defined human pluripotent stem cell-derived microglia and tri-culture system model C3 production in Alzheimer’s disease
AUTHORS: Sudha R. Guttikonda, Lisa Sikkema, Jason Tchieu, Nathalie Saurat, Ryan Walsh, Oliver Harschnitz, Gabriele Ciceri, Marjolein Sneeboer, Linas Mazutis, Manu Setty, Paul Zumbo, Doron... | ["[Derivation of microglia from hPSCs]\nDissociate hPSCs maintained in Essential 8 medium by Accutase to obtain a single-cell suspension.", "[Derivation of microglia from hPSCs]\nPlate a total of 60,000 cells per cm2 in E8 medium containing activin A (R&D 338-AC; ), BMP4 (R&D; ), CHIR 99021 (Tocris; ) and ROCK inhibito... |
80,232 | Electrodes fabrication on Kapton film with NEJE mini laser - L-Cu1.1 | 1 | dx.doi.org/10.17504/protocols.io.kxygx9bykg8j/v1 | https://www.protocols.click/view/electrodes-fabrication-on-kapton-film-with-neje-mi-cskgwctw | David Bahamon Pinzon, Catherine Bergman, Dvanega | TITLE: Electrodes fabrication on Kapton film with NEJE mini laser - L-Cu1.1
AUTHORS: David Bahamon Pinzon, Catherine Bergman, Dvanega
[DESCRIPTION]
This protocol describes the fabrication of laser inscribed graphene (LIG) electrodes on polyimide film (i.e., Kapton film) using the NEJE mini laser with copper electrodep... | ["[Procedure] Prepare Substrate\n\na. Cut a 2\" by 5\" (5cm x 5cm) sample of kapton film.\nb. Place a few drops of isopropyl alcohol on a Kimwipe and clean the surface.\n\n \n\nc. Place the sample onto the center of the laser platform (as shown in figure 2A)\n \nd. Ensure that the workpiece is flat. If the workpiec... |
51,250 | Sample collection and eDNA extraction from Sterivex filter units | 4 | dx.doi.org/10.17504/protocols.io.bwaspaee | https://www.protocols.io/view/sample-collection-and-edna-extraction-from-sterive-bwaspaee | Oscar Chiang, Pedro Inostroza | TITLE: Sample collection and eDNA extraction from Sterivex filter units
AUTHORS: Oscar Chiang, Pedro Inostroza
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The following workflow covers several steps in the DNA analysis of environmental samples, from the water collection to the analysis bac... | ["[DNA extraction ]\nPlace the Sterivex vertically (with the inlet cap upward) and load of ST1B buffer. ST1B is stored at . Be careful putting the pipette tip through the inlet (orange cap). Dispense the buffer slowly; a fraction of the volume can be lost.\n900 µl\n4 °C", "[DNA extraction ]\nAllow mixing in a vortex wi... |
57,520 | Data normalisation of RT-qPCR data for detection of SARS-CoV-2 in wastewater | 5 | dx.doi.org/10.17504/protocols.io.b4eqqtdw | https://www.protocols.io/view/data-normalisation-of-rt-qpcr-data-for-detection-o-b4eqqtdw | Adrian Roberts, Zhou Fang, Claus-Dieter Mayer, Anastasia Frantsuzova, Graeme J Cameron, Livia C T Scorza | TITLE: Data normalisation of RT-qPCR data for detection of SARS-CoV-2 in wastewater
AUTHORS: Adrian Roberts, Zhou Fang, Claus-Dieter Mayer, Anastasia Frantsuzova, Graeme J Cameron, Livia C T Scorza
[DESCRIPTION]
After obtaining the raw measurements as gene copies per litre using RT-qPCR, a normalisation process is re... | ["[Decision tree] Normalisation requires population size and water flow at the collection site. \n\nDepending on the level of information available for particular site and date (such as ammonia content in wastewater or historical flow) different processing paths are available, as described below in the step by step alg... |
27,429 | Exercise experiences in patients with lung cancer patients: A qualitative approach | 1 | dx.doi.org/10.17504/protocols.io.62dhga6 | https://www.protocols.io/view/exercise-experiences-in-patients-with-lung-cancer-62dhga6 | Pi-Hua Chang, Ching-Rong Lin, Yun-Hsiang Lee, Yi-Lin Liu, Gee-Chen Chang, Yeur-Hur Lai, Pi-Hua Chang, Taichung Veterans General Hospital | TITLE: Exercise experiences in patients with lung cancer patients: A qualitative approach
AUTHORS: Pi-Hua Chang, Ching-Rong Lin, Yun-Hsiang Lee, Yi-Lin Liu, Gee-Chen Chang, Yeur-Hur Lai, Pi-Hua Chang, Taichung Veterans General Hospital
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Background Pat... | ["The inclusion criteria were as follows: (1) older than age 20 years; (2) diagnosed with metastatic lung cancer; (3) spoke Chinese or Taiwanese; (4) had exercise habits or behaviors; (5) admitted in our hospital; and (6) understood the research purpose and agreed to participate in the study.", "The exclusion criteria ... |
null | null | null | dx.doi.org/10.17504/protocols.io.cpevjd | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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44,920 | A Case of Congenital Hereditary Metabolic Disease-urea Cycle Metabolic Disorder | 4 | null | https://www.protocols.io/view/a-case-of-congenital-hereditary-metabolic-disease-bp4ymqxw | 181830691 , sdadf | TITLE: A Case of Congenital Hereditary Metabolic Disease-urea Cycle Metabolic Disorder
AUTHORS: 181830691 , sdadf
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Congenital metabolic diseases are caused by the lack or abnormality of a certain enzyme or its cofactors, which can cause accumulation or ... | [] |
41,476 | Measuring the amuont of bacteria in a soil sample | 6 | dx.doi.org/10.17504/protocols.io.bkrckv2w | https://www.protocols.io/view/measuring-the-amuont-of-bacteria-in-a-soil-sample-bkrckv2w | Andreea S | TITLE: Measuring the amuont of bacteria in a soil sample
AUTHORS: Andreea S
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Colony Forming Units (c.f.u) is a unit that is used in microbiology to estimate the number of viable bacteria or fungal cells in a sample. It also depends on their abilit... | ["[CFU determination]\nColony Forming Units (CFU) can be determined by estimating the OD of spore suspension using a tube-reading spectrophotometer adjusted at 1.978 [corresponding to 8.5 · 1010 CFU/ml] at 600nm absorbance wavelength", "[CFU determination]\nThe formulation will be placed on sterile aluminum foil in pan... |
92,257 | Code-barres natif des amplicons (plaques 96 puits) | 1 | dx.doi.org/10.17504/protocols.io.81wgbxw61lpk/v1 | https://www.protocols.io/view/code-barres-natif-des-amplicons-plaques-96-puits-c6b9zar6 | Alex Shaw, Catherine Troman, Joyce Akello, Erika Bujaki, Javier Martin, Nick Grassly | TITLE: Code-barres natif des amplicons (plaques 96 puits)
AUTHORS: Alex Shaw, Catherine Troman, Joyce Akello, Erika Bujaki, Javier Martin, Nick Grassly
[DESCRIPTION]
Le protocole suivant concerne la préparation des amplicons pour le séquençage à l'aide du kit de codage à barres Oxford Nanopore Native version 14 avec 9... | ["[Preparation de l'ADN d'entree] Quantifier l'ADN amplifié avec un kit “Qubit Broad Range dsDNA”.", "[Preparation de l'ADN d'entree] En bref, créer un master mix de 200 μl (199 μl de tampon, 1 μl de réactif Qubit) pour chaque échantillon + 2 standards + 10 %. Pour les deux standards, ajouter 190 μl... |
null | null | null | dx.doi.org/10.17504/protocols.io.nrxdd7n | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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89,318 | Estimation of uncertainty in calculations of apparent iron solubility in seawater | 1 | dx.doi.org/10.17504/protocols.io.rm7vzxjzrgx1/v2 | https://www.protocols.io/view/estimation-of-uncertainty-in-calculations-of-appar-c3geyjte | Kechen Zhu, Mark James Hopwood, Martha Gledhill | TITLE: Estimation of uncertainty in calculations of apparent iron solubility in seawater
AUTHORS: Kechen Zhu, Mark James Hopwood, Martha Gledhill
[DESCRIPTION]
The apparent iron (Fe) solubility (SFe(III)app) was calculated via an ion paring-organic matter (NICA-Donnan) model at ambient pH, temperature and dissolved or... | ["[Run the speciation code ORCHESTRA in parallel with code PEST++] Set up calculations of iron speciation and solubility in seawater via the speciation code ORCHESTRA.", "[Run the speciation code ORCHESTRA in parallel with code PEST++] In the same sub-folder of ORCHESTRA, write the code for combining PEST++ to ORCHESTR... |
null | null | null | dx.doi.org/10.17504/protocols.io.dt96r5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
The Qiagen QIAquick Gel Extraction kit (catalog #28704 and 28706) are for extraction of DNA fragments (70 bp – 10 kb) from standard or low-melt agarose gels in TAE buffer (Tris·acetate/EDTA) or TBE buffer (Tris·borate/ EDTA) and DNA cleanup from enzymatic reactions. The kit is s... | [] |
90,896 | PlatereaderPCAoxidationAssay | 4 | dx.doi.org/10.17504/protocols.io.bp2l6xm6dlqe/v1 | https://www.protocols.io/view/platereaderpcaoxidationassay-c4zqyx5w | Lev Tsypin, Dianne K Newman, Allen W Chen, Scott Saunders | TITLE: PlatereaderPCAoxidationAssay
AUTHORS: Lev Tsypin, Dianne K Newman, Allen W Chen, Scott Saunders
[DESCRIPTION]
Protocol for measuring phenazine-1-carboxylic acid oxidation in a plate reader
[STEPS]
SECTION: Pre-grow cultures for assay
1. Two days before, streak frozen culture stock on LB agar plate, grow over n... | ["[Pre-grow cultures for assay] Two days before, streak frozen culture stock on LB agar plate, grow over night at 30 ºC; inoculate liquid cultures for next step with a mixed patch of cells.", "[Pre-grow cultures for assay] Grow 5 mL cultures of cells overnight at 30 ºC in LB for 17 hours +/- 10 minutes.", "[Pre-grow cu... |
null | null | null | dx.doi.org/10.17504/protocols.io.re4d3gw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Testing for metal toxicity as a result of addition of a putative phosphate transporter to a <em>S. cerevisiae</em> Δ<em>pho84</em> strain</p>
[STEPS]
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44,754 | CELL COUNT- 02 - Manual cell count with Türk Solution | 4 | dx.doi.org/10.17504/protocols.io.bpxsmpne | https://www.protocols.io/view/cell-count-02-manual-cell-count-with-t-rk-solution-bpxsmpne | Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino | TITLE: CELL COUNT- 02 - Manual cell count with Türk Solution
AUTHORS: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Published work using this protocol:</div><div class = "text-blo... | ["Use Türk solution for checking cell purity.Mix of cell suspention with an equal amount of Türk solution (dilution factor = 2), allow mixture 3 min at room temperature.\n10 µl\n{\"blocks\":[{\"key\":\"9lo9p\",\"text\":\"This recepe is used in the following protocols:\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyle... |
89,215 | Human Blood Sample Collection Protocol --University of Minnesota TMCs | 1 | dx.doi.org/10.17504/protocols.io.n2bvj327nlk5/v1 | https://www.protocols.io/view/human-blood-sample-collection-protocol-university-c3c7yizn | Laura J Niedernhofer, David A Bernlohr | TITLE: Human Blood Sample Collection Protocol --University of Minnesota TMCs
AUTHORS: Laura J Niedernhofer, David A Bernlohr
[DESCRIPTION]
Collection protocol obtained from the attached BioNet Specimen Procurement Agreement provided by the UMN CTSI Biorepository and Laboratory Services (BLS).
[STEPS]
SECTION: Pr... | ["[Preparation] Patient Identification: As soon as a patient is scheduled, the research team will email bionet@umn.edu a completed Specimen Procurement Request Form.", "[Preparation] Patient Consent: Researcher consents. The original signed consent form will be placed in the patient chart and scanned into Epic. BioNet ... |
54,230 | PCR protocol for gene COXI neo-caledonian freshwater micro-crustaceans | 4 | dx.doi.org/10.17504/protocols.io.261ge4y4jv47/v1 | https://www.protocols.io/view/pcr-protocol-for-gene-coxi-neo-caledonian-freshwat-by7wpzpe | Coline Royaux | TITLE: PCR protocol for gene COXI neo-caledonian freshwater micro-crustaceans
AUTHORS: Coline Royaux
[DESCRIPTION]
This PCR protocol has been used to amplify the Cytochrome Oxydase I gene of neo-caledonian genera Boeckella, Lynceus, Eulimnadia and Streptocephalus with several primers.
[STEPS]
1. Prepare the mix for t... | ["Prepare the mix for the PCR depending on the quantity of DNA samples you want to amplify", "For each well, mix 12.44 µL, 2 µL, 1 µL, 1 µL, 0.8 µL and 0.12 µL. This mix is hereafter named \"intermediary mix\".", "Add your primers to the mix, 0.32 µL 10 picomolar (pM) and 0.32 µL 10 picomolar (pM) for each well. This ... |
null | null | null | dx.doi.org/10.17504/protocols.io.e3pbgmn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>T regulatory cells (also known as Tregs or Regulatory T cells) are essential cells in<br />the immune system that suppress immune responses of other cells, designed to<br />limit excessive reactions and prevent autoimmunity. Tregs are characterized by the<br />expression of C... | [] |
79,230 | cermep-bids-retro | 5 | dx.doi.org/10.17504/protocols.io.261ge319dl47/v1 | https://www.protocols.io/view/cermep-bids-retro-crk6v4ze | lucie.chalet | TITLE: cermep-bids-retro
AUTHORS: lucie.chalet
[DESCRIPTION]
cermep-bids-retro enables the formatting of retrospective PET and MRI data to BIDS standards from DICOM databases. When dealing with pre-clinical imaging modalities, numerous metadata are overlooked during acquisitions making it difficult to automatically fo... | ["[cermep-bids-retro installation] Clone repository\nIn GitBash:", "[cermep-bids-retro installation] Create conda environment", "[Fill-in input files] This step is key to a functional method. It requires a good knowledge\nof the available tags and fields in the DICOM data and one can always refer\nto the BIDS specifica... |
null | null | null | dx.doi.org/10.17504/protocols.io.rhhd336 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A real-time PCR for the detection of Coxiella burnetii DNA targeting the IS1111a gene. The assay is based on a published method by Banazis et al 2010, using a different PCR kit. The oligonucleitide sequences have not been modified however the concentration have been optimise... | [] |
21,874 | ROS staining for Arabidopsis (green fluorescent stain) | null | dx.doi.org/10.17504/protocols.io.zksf4we | null | Magdalena Julkowska | TITLE: ROS staining for Arabidopsis (green fluorescent stain)
AUTHORS: Magdalena Julkowska
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is adapted from two publications describing fluorescent staining for ROS - </span><a style = "text-decoration:underline;color:blue;cursor:poi... | ["Transfer the seedlings from agar plates into nutrient solution that is the same as agar plate composition (but without Dashin agar). You can use 24/12/6 well-plates - this will depend on your final seedlings size", "Wash the seedlings with medium without DCF-DA", "Sterilize the seedlings, germinate and transfer to fo... |
42,158 | Influenza A Virus-Infected Lung Epithelial Cell Co-Culture with Human Peripheral Blood Mononuclear Cells | 4 | dx.doi.org/10.17504/protocols.io.bmenk3de | https://www.protocols.io/view/influenza-a-virus-infected-lung-epithelial-cell-co-bmenk3de | Liyen Loh, Marios Koutsakos, Katherine Kedzierska, Timothy S. C. Hinks | TITLE: Influenza A Virus-Infected Lung Epithelial Cell Co-Culture with Human Peripheral Blood Mononuclear Cells
AUTHORS: Liyen Loh, Marios Koutsakos, Katherine Kedzierska, Timothy S. C. Hinks
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Sensing of influenza A virus (IAV) infection by pattern reco... | ["[IAV Infection of Human Lung Epithelial Cell Line, A549]\nprior to infection, in two T75 flasks, seed 5 x 106 A549 cells in a total volume of .\n[media]\nOne flask for IAV infection and the second flask for uninfected control A549s.", "[IAV Infection of Human Lung Epithelial Cell Line, A549]\nOn the day of infection:... |
79,212 | Symbiotic Dose-50 (SD50) for Vibrio fischeri strain to colonize Euprymna scolopes | 4 | dx.doi.org/10.17504/protocols.io.yxmvm2155g3p/v1 | https://www.protocols.click/view/symbiotic-dose-50-sd50-for-vibrio-fischeri-strain-crkkv4uw | ard, ejg, agc, Tim I Miyashiro | TITLE: Symbiotic Dose-50 (SD50) for Vibrio fischeri strain to colonize Euprymna scolopes
AUTHORS: ard, ejg, agc, Tim I Miyashiro
[DESCRIPTION]
This protocol details symbiotic dose-50 (SD50) for Vibrio fischeri strain to colonize Euprymna scolopes.
[STEPS]
SECTION: Preparation of V. fischeri Cultures
1. For each strai... | ["[Preparation of V. fischeri Cultures] For each strain of interest, initiate a starter culture by inoculating 3 mL LBS with an isolated colony. Incubate starter cultures (~16 h) at 28 °C shaking at .", "[Preparation of V. fischeri Cultures] Measure the OD600 of each starter culture. In a microfuge tube, normalize ... |
38,388 | Zebrafish Embryo Dissociation for MACS | 4 | dx.doi.org/10.17504/protocols.io.bhquj5ww | https://www.protocols.io/view/zebrafish-embryo-dissociation-for-macs-bhquj5ww | Sam Wattrus | TITLE: Zebrafish Embryo Dissociation for MACS
AUTHORS: Sam Wattrus
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Method of zebrafish embryo dissociation and microbead binding for magnetic enrichment by MACS. </div></div>
[STEPS]
?. Prepare enzyme mix by adding 200ul Enzyme H, 100ul Enzyme R, and ... | ["Prepare enzyme mix by adding 200ul Enzyme H, 100ul Enzyme R, and 25ul Enzyme A to 4.7mL DMEM on ice.", "Tricaine and transfer embryos in minimal E3 to plate lid. Remove excess E3 (can be done effectively by blocking embryos with razor blade and wicking up water behind the blade with a Kimwipe). Chop embryos in plate ... |
49,110 | TBK1 knockdown and rescue in Hela-M cells | 4 | dx.doi.org/10.17504/protocols.io.bt7wnrpe | https://www.protocols.io/view/tbk1-knockdown-and-rescue-in-hela-m-cells-bt7wnrpe | OLIVIA HARDING, Olivia Harding, Erika L.F: Holzbaur | TITLE: TBK1 knockdown and rescue in Hela-M cells
AUTHORS: OLIVIA HARDING, Olivia Harding, Erika L.F: Holzbaur
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">TANK-binding kinase 1 (TBK1) is a multifunctional kinase with roles in several crucial cell processes, including innate immune response, anti... | ["[Day 1: Plating]\nTrypsinize Hela-M cells by aspirating all media from a 10 cm dish of confluent cells, then dropping onto cells.\n[Trypsin]", "[Day 1: Plating]\nIncubate cells at , for.\n37 °C\n[CO2]", "[Day 1: Plating]\nResuspend detached cells and neutralize Trypsin with with and for a final volume of .\n[DME... |
null | null | null | dx.doi.org/10.17504/protocols.io.e2gbgbw | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p><strong>Tips</strong>:</p>
<p><strong>High background</strong></p>
<p>1. Transfer buffers may have become contaminated. Contamination can be transferred to the blots from electrophoresis and related equipment used in blot preparation.</p>
<p>2. Post-antibody washes may not hav... | [] |
89,851 | LRRK2 thermal shift assay | 4 | dx.doi.org/10.17504/protocols.io.kxygx3y6kg8j/v1 | https://www.protocols.io/view/lrrk2-thermal-shift-assay-c3y3ypyn | Verena Dederer, Deep Chatterjee, Sebastian Mathea, Stefan Knapp | TITLE: LRRK2 thermal shift assay
AUTHORS: Verena Dederer, Deep Chatterjee, Sebastian Mathea, Stefan Knapp
[DESCRIPTION]
Thermal shift assay or differential scanning fluorimetry analyzes the effect of small molecules on the thermostability of a protein by gradual heat denaturation and monitoring absorption of the fluor... | ["[Fluorescent-based thermal shift assay] Prepare 4 µM master mix of protein in buffer (20 mM Hepes pH 7.4, 150 mM NaCl, 5% glycerol) and add 1:1000 dilution of SYPR Orange.", "[Fluorescent-based thermal shift assay] Aliquot 20 µL of the master mix into a white 96 well plate.", "[Fluorescent-based thermal shift assay] ... |
null | null | null | dx.doi.org/10.17504/protocols.io.hhvb366 | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?. | [] |
22,659 | Leaf sampling for hydrogen cyanide determination in cassava leaves | null | dx.doi.org/10.17504/protocols.io.2dbga2n | null | Matema Imakumbili | TITLE: Leaf sampling for hydrogen cyanide determination in cassava leaves
AUTHORS: Matema Imakumbili
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how leaf samples from cassava plants are to be collected for total hydrogen cyanide determination in cassava leaves. The protoc... | ["[Plant selection before leaf sampling]\nFour plants of the same cassava variety must be selected on a field or experimental plot. This is why pot experiments need to be replicated at least four times, to produce a minimum of four plants per treatment for cyanide determination in cassava leaves. Four plants of the sam... |
81,855 | HSQC_15N.nan | 5 | dx.doi.org/10.17504/protocols.io.q26g7yob9gwz/v1 | https://www.protocols.io/view/hsqc-15n-nan-ct67wrhn | NAN KB, Alex Eletsky, John Glushka | TITLE: HSQC_15N.nan
AUTHORS: NAN KB, Alex Eletsky, John Glushka
[DESCRIPTION]
This protocol describes running a 2D 15N HSQC pulse sequence with sensitivity enhancement, gradient coherence selection and water flip-back. This produces a 2D phase-sensitive 15N-1H correlation dataset that displays signals for each backbon... | ["[Create 15N HSQC experiment] Start with existing Dataset containing 1D PRESAT data in EXPNO 1 collected with protocol PRESAT_bio.nan", "[Create 15N HSQC experiment] Click OK at bottom of window to create the new EXPNO directory.\nIt will be the active experiment in the acquisition window and should now be listed on y... |
101,710 | Assembly and Operation of a Custom Carbon Dioxide and Air Gassing Manifold for Growth of Photoautotrophic Algal Cultures in Illuminated Incubators. | 0 | dx.doi.org/10.17504/protocols.io.6qpvr897blmk/v1 | https://www.protocols.io/view/assembly-and-operation-of-a-custom-carbon-dioxide-dfjn3kme | Dimitrios Camacho, Sabeeha Merchant | TITLE: Assembly and Operation of a Custom Carbon Dioxide and Air Gassing Manifold for Growth of Photoautotrophic Algal Cultures in Illuminated Incubators.
AUTHORS: Dimitrios Camacho, Sabeeha Merchant
[DESCRIPTION]
This protocol describes a method for setting up and operating an apparatus to enrich air with 5% CO2 for ... | ["[Maintenance] 23.3. Soak used foam plugs in soap and water. \n\n23.3. Rinse thoroughly and squeeze remaining water out of the foam stoppers.\n\n23.3. Air dry and then wrap in aluminum foil and autoclave to re-use.", "[Maintenance] Autoclave sterilize tubes and connections.\n\n22.1. Do not autoclave the aquarium pump,... |
103,178 | Proteomic Sample Preparation | 0 | dx.doi.org/10.17504/protocols.io.261ge5x4og47/v1 | https://www.protocols.io/view/proteomic-sample-preparation-dgzi3x4e | Shiyi Wang | TITLE: Proteomic Sample Preparation
AUTHORS: Shiyi Wang
[DESCRIPTION]
Proteomic Sample Preparation
[STEPS]
1. **Sample Storage and Preparation** - Received 12 samples (3 of each WT CYT, GS CYT, WT EZR, and GS EZR) and kept at -80°C until processing. - Spike samples with undigested bovine casein at a total of either 1... | ["**Sample Storage and Preparation** - Received 12 samples (3 of each WT CYT, GS CYT, WT EZR, and GS EZR) and kept at -80°C until processing. - Spike samples with undigested bovine casein at a total of either 1 or 2 pmol as an internal quality control standard.", "**Reduction and Alkylation** - Reduce samples for 15 mi... |
null | null | null | dx.doi.org/10.17504/protocols.io.psednbe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>osmFISH is a cyclic single molecule fluorescent<em> in situ</em> hybridization protocol used to quantify the expression level of specific transcripts in tissue sections by direct labeling of individual RNA molecules. The number of transcripts quantified in each round correspo... | [] |
57,838 | Nucleofection (Amaxa) and electroporation (Biorad) of hPSCs | 2 | dx.doi.org/10.17504/protocols.io.b4qnqvve | https://www.protocols.io/view/nucleofection-amaxa-and-electroporation-biorad-of-b4qnqvve | Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner | TITLE: Nucleofection (Amaxa) and electroporation (Biorad) of hPSCs
AUTHORS: Hanqin Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner
[DESCRIPTION]
This collection describes the standard procedure for the delivery of plasmids, mRNA or ribonucleoprotein (RNP) into human pluripotent stem cells (hPSCs) usi... | [] |
38,914 | A scoping review of “remote” rehabilitation interventions to address COVID-19 sequalae | 1 | dx.doi.org/10.17504/protocols.io.bh9aj92e | https://www.protocols.io/view/a-scoping-review-of-remote-rehabilitation-interven-bh9aj92e | Julie Whitney, Lindsay Bearne, Patrick White, Arietta Spinou, Emma Godfrey, Matthew O'Connell, Julia Fox-Rushby, Graham Fisher, Katie Sheehan | TITLE: A scoping review of “remote” rehabilitation interventions to address COVID-19 sequalae
AUTHORS: Julie Whitney, Lindsay Bearne, Patrick White, Arietta Spinou, Emma Godfrey, Matthew O'Connell, Julia Fox-Rushby, Graham Fisher, Katie Sheehan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Plain E... | ["Protocol registrationThe protocol is registered on protocols.io.", "Inclusion criteriaPapers / applications that describe a rehabilitation intervention:that is aimed at long-term symptoms known to be associated with COVID-19 (i.e. fatigue, breathlessness, weakness)aimed at community based or self-management level of ... |
23,876 | NADH Oxidase Activity | null | dx.doi.org/10.17504/protocols.io.3jcgkiw | null | Eva Feldman | TITLE: NADH Oxidase Activity
AUTHORS: Eva Feldman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Describes assay to quantitate NADH Oxidase activity from tissues. </div><div class = "text-block"><span style = "font-we... | ["[Sample Preparation:]\nTurn on Multiskan, set temp to 37ºC and set up plate layout.", "[Sample Preparation:]\nSonicate tissue on ice in 20mM PB pH 7.4 with PMSF inhibitor or thaw prepared samples on ice.", "[Sample Preparation:]\nRemove 25µL for protein analysis.", "[Sample Preparation:]\nPrepare NADH, enough for who... |
16,606 | PCR Protocol for chicken sex identification. | null | dx.doi.org/10.17504/protocols.io.uf6etre | null | Liyan He, Priscila Martins, Joris Huguenin, Thi-Nhu-Ngoc Van, Taciana Manso, Therese Galindo, Lise Catherinot, Franck Molina, Julien Espeut | TITLE: PCR Protocol for chicken sex identification.
AUTHORS: Liyan He, Priscila Martins, Joris Huguenin, Thi-Nhu-Ngoc Van, Taciana Manso, Therese Galindo, Lise Catherinot, Franck Molina, Julien Espeut
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is an invasive PCR based chicken gender determ... | ["[Prepare the Primers Ddilutions]\nTwo set of primers (12S & SWIM) are used in this protocol for positive control (12S) and female indication (SWIM). \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... |
84,767 | Bioinformatic workflow for the analysis of SARS-CoV-2 Spike sequencing raw data from wastewater | 5 | dx.doi.org/10.17504/protocols.io.4r3l2244xl1y/v1 | https://www.protocols.click/view/bioinformatic-workflow-for-the-analysis-of-sars-co-cwz7xf9n | Ana C Reis, Daniela Pinto, Mónica V. Cunha | TITLE: Bioinformatic workflow for the analysis of SARS-CoV-2 Spike sequencing raw data from wastewater
AUTHORS: Ana C Reis, Daniela Pinto, Mónica V. Cunha
[DESCRIPTION]
This protocol describes the bioinformatics procedure to analyse SARS-CoV-2 Spike Illumina sequencing data from wastewater. This workflow can be applie... | ["[Create work directory and organize raw data] Import and organize the fastq.gz raw data files.", "[Examine read quality] FastQC is a quality control tool for high throughput sequence data which assesses multiple metrics and provides a QC report. FastQC (Galaxy version 0.11.9) is used for preliminary read quality asse... |
null | null | null | dx.doi.org/10.17504/protocols.io.gurbwv6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This collection contains two protocols, one for Western Blot Detection and the other for ICW Detection.
[STEPS] | [] |
87,303 | Sanger Tree of Life HMW DNA Extraction: Manual Mollusc Nanobind® | 4 | dx.doi.org/10.17504/protocols.io.14egn36nyl5d/v1 | https://www.protocols.io/view/sanger-tree-of-life-hmw-dna-extraction-manual-moll-czhfx33n | Pacific Biosciences, Adam AB Bates, Caroline Howard | TITLE: Sanger Tree of Life HMW DNA Extraction: Manual Mollusc Nanobind®
AUTHORS: Pacific Biosciences, Adam AB Bates, Caroline Howard
[DESCRIPTION]
This protocol describes the manual extraction of HMW DNA from mollusc samples intended for long-read sequencing using the Nanobind® tissue kit and following the ‘Extracting... | ["[Laboratory protocol] Transfer tissue to a 2 mL microcentrifuge tube or a powermash tube if not cryoprepped and add \n750 μL ice cold buffer CT; powermashing if required.", "[Laboratory protocol] Centrifuge 6,000 × g at 4 °C for 5 minutes.", "[Laboratory protocol] Discard supernatant and add fresh 1 mL cold buffer CT... |
44,131 | Preparing hPSC-derived neurons for single-cell RNA sequencing | 1 | dx.doi.org/10.17504/protocols.io.bpcbmisn | https://www.protocols.io/view/preparing-hpsc-derived-neurons-for-single-cell-rna-bpcbmisn | Cortina Chen, Florian T Merkle | TITLE: Preparing hPSC-derived neurons for single-cell RNA sequencing
AUTHORS: Cortina Chen, Florian T Merkle
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is about Preparing hPSC-derived neurons for single-cell RNA sequencing.</div></div>
[STEPS]
?. Prepare dissociation solution and... | ["Prepare dissociation solution and wash buffers.", "Wash cells 2x with DPBS.", "Add dissociation solution ( for 6 well plate, for 24 well plate).\n1 mL\n250 µl", "Incubate at for up to until cells are ready to detach easily (test by pipetting dissociation solution onto cells with P1000, check every ).\n37 °C", "Det... |
26,678 | BestRAD protocol | null | dx.doi.org/10.17504/protocols.io.6awhafe | null | Thom Nelson | TITLE: BestRAD protocol
AUTHORS: Thom Nelson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Modified from protocol of Sean O’Rourke and Mike Miller published in:</div></div>
[STEPS]
?. [Part 1 - Digestion and BestRAD adaptor ligation]
I. Restriction DigestDilute genomic DNA samples to a common con... | ["[Part 1 - Digestion and BestRAD adaptor ligation]\nI. Restriction DigestDilute genomic DNA samples to a common concentration.Add (50-100 ng) of genomic DNA to each well of a 96-well PCR plate.\n10 µl", "[Part 1 - Digestion and BestRAD adaptor ligation]\nPlease select between the two following options: performing she... |
79,109 | Dual antibody immunohistochemistry staining | 4 | dx.doi.org/10.17504/protocols.io.81wgbyoryvpk/v1 | https://www.protocols.io/view/dual-antibody-immunohistochemistry-staining-crhdv326 | Angelina Spence, Mako Goldston, Kausalia Vijayaragavan, Marc Bosse, Sean Bendall, Mike Angelo | TITLE: Dual antibody immunohistochemistry staining
AUTHORS: Angelina Spence, Mako Goldston, Kausalia Vijayaragavan, Marc Bosse, Sean Bendall, Mike Angelo
[DESCRIPTION]
This protocol provides guidelines to perform dual antibody immunohistochemistry ( IHC) on standard FFPE tissue in the Sean C. Bendall and Michael R. An... | ["[Protocol IO references] This protocol refers to detailed procedures found in these respective Protocol IO: \nIHC staining dx.doi.org/10.17504/protocols.io.bf6ajrae\nSequenza dx.doi.org/10.17504/protocols.io.bmc6k2ze\nMIBI and IHC solutions dx.doi.org/10.17504/protocols.io.bmc6k2ze", "[Slide preparation] Slides are b... |
null | null | null | dx.doi.org/10.17504/protocols.io.hheb33e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is part of the manuscript: <a href="http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2000862" target="_blank">Gonçalves et al. Commensal bacteria and essential amino acids control food choice behavior and reproduction. Plos Biology. 2017 Apr ... | [] |
83,216 | Generation of ATG3 KO Hela cells stably expressing HaloTag-LC3B | 4 | dx.doi.org/10.17504/protocols.io.5qpvo3xq9v4o/v1 | https://www.protocols.click/view/generation-of-atg3-ko-hela-cells-stably-expressing-cvhqw35w | Xuefeng Ren | TITLE: Generation of ATG3 KO Hela cells stably expressing HaloTag-LC3B
AUTHORS: Xuefeng Ren
[DESCRIPTION]
This protocol details generation of ATG3 KO Hela cells stably expressing HaloTag-LC3B.
[STEPS]
SECTION: Procedures
1. Transform each plasmid into Stbl3 competent cells for the propagation. Next day, pick up one ... | ["[Procedures] Transform each plasmid into Stbl3 competent cells for the propagation. Next day, pick up one colony to inoculate culture in LB medium with ampicillin.", "[Procedures] Midi prep the cultures to purify plasmids (Qiagen).", "[Procedures] Plate 5 x 106 HEK 293T cells on a 10 cm plate in DMEM medium.", "[P... |
63,299 | 10x ATAC Genomics Sample Processing | 1 | dx.doi.org/10.17504/protocols.io.14egn7ndmv5d/v1 | https://www.protocols.io/view/10x-atac-genomics-sample-processing-b93br8in | Allen Institute for Brain Science | TITLE: 10x ATAC Genomics Sample Processing
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
Protocol is used to profile all the open chromatin regions at a single nuclei level through the rapid generation of NGS-ready libraries from a pool of transposed nuclei.
[STEPS] | [] |
69,873 | Cylinder behavioral test | 4 | dx.doi.org/10.17504/protocols.io.j8nlkw58dl5r/v1 | https://www.protocols.io/view/cylinder-behavioral-test-cggrttv6 | miquel.vila | TITLE: Cylinder behavioral test
AUTHORS: miquel.vila
[DESCRIPTION]
Cylinder behavioral testfor left and right forepaw use
[BEFORE_START]
All behavioral tests have to be performed during the light cycle by an investigator blinded to the experimental groups.
[GUIDELINES]
Important: Rats that present an asymmetric usag... | ["First allow rats to habituate to the experimental room for at least 1 h before each test.", "Put rats in a glass cylinder and the total number of left and right forepaw touches performed within 5 min was counted.", "Clean behavioral equipment with 70% ethanol after each test session to avoid olfactory cues."] |
98,468 | Food Security And Self Sufficiency Program In Mo’orea | 0 | dx.doi.org/10.17504/protocols.io.n2bvjnykbgk5/v2 | https://www.protocols.io/view/food-security-and-self-sufficiency-program-in-mo-o-dcec2taw | Nohea Rodriguez | TITLE: Food Security And Self Sufficiency Program In Mo’orea
AUTHORS: Nohea Rodriguez
[DESCRIPTION]
This research aims to investigate the impact of food dependency on local livelihoods in Mo’orea in terms of nutrition and food accessibility. Through a culturally sensitive and community-based diet program (The Mo'orea ... | ["[The Mo'orea Diet Program] Interview communities throughout Mo’orea for insight on food consumption patterns, barriers to accessing local foods, and perceptions of policy interventions.", "[The Mo'orea Diet Program] Identify key Tahitian foods and dietary practices that can be incorporated into current diet... |
11,895 | Semi-dry western blot and chemiluminescent detection | 1 | dx.doi.org/10.17504/protocols.io.puxdnxn | https://www.protocols.io/view/semi-dry-western-blot-and-chemiluminescent-detecti-puxdnxn | Douglas Adamoski, Sandra Martha Gomes Dias | TITLE: Semi-dry western blot and chemiluminescent detection
AUTHORS: Douglas Adamoski, Sandra Martha Gomes Dias
[STEPS]
SECTION: Sample preparation and SDS-PAGE
4. Prepare your samples and run SDS-PAGE as usual.
SECTION: Semi-dry transfer preparation
5. Dilute Timmons-Dunbar Buffer 1X using ultrapure water. Usually, 5... | ["[Sample preparation and SDS-PAGE] Prepare your samples and run SDS-PAGE as usual.", "[Semi-dry transfer preparation] Dilute Timmons-Dunbar Buffer 1X using ultrapure water. Usually, 50 mL for each mini gel (8.4cm x 7cm) to be transfered are enough.", "[Blocking and antibody incubation] Immediately transfer the membran... |
73,796 | Tail Clipping Larval Zebrafish | 4 | null | https://www.protocols.io/view/tail-clipping-larval-zebrafish-ckbcusiw | FishFloorUCL | TITLE: Tail Clipping Larval Zebrafish
AUTHORS: FishFloorUCL
[DESCRIPTION]
Tail clipping of ~ 2–4 dpf zebrafish larvae for genotyping.
[STEPS]
SECTION: Introduction
1. On FishFloor UCL, Gareth Powell would be the best person to ask for a live demonstration.
Technique originally published by Kosuta et al (2018) – vide... | ["[Introduction] On FishFloor UCL, Gareth Powell would be the best person to ask for a live demonstration.\n\nTechnique originally published by Kosuta et al (2018) – video protocol:\n\nhttps://www.jove.com/v/58024/high-throughput-dna-extraction-genotyping-3dpf-zebrafish-larvae-fin\n\nKosuta, C., et al. (2018). “High-th... |
100,188 | HTTM : Transposon mutagenesis | 4 | dx.doi.org/10.17504/protocols.io.36wgq72n3vk5/v4 | https://www.protocols.io/view/httm-transposon-mutagenesis-dd3428qw | Antoine Champie, Amélie De Grandmaison, Sebastien Rodrigue | TITLE: HTTM : Transposon mutagenesis
AUTHORS: Antoine Champie, Amélie De Grandmaison, Sebastien Rodrigue
[DESCRIPTION]
Part of the HTTM protocol dedicated to the transposon mutagenesis of targets cells.
The last step in this version contains a supplemental video with extra context and tips, as part of the protocols... | ["[Day 1] (1-A) Make a 15 mL LB (Diaminopimelic acid [Dap], Ampicillin [Amp], Spectinomycin [Spec]) pre-culture ( 2 mL per plate minimum) of the donor strain eAC494 and incubate with agitation at 37 °C overnight.", "[Day 1] (1-B) Prepare the 96 deep-well plates for conjugation :", "[Day 1] Preheat the deep-well plates ... |
56,468 | MAS-ISO-seq - from 10x Single Cell Gene Expression Libraries | 4 | dx.doi.org/10.17504/protocols.io.kqdg3p5ezl25/v1 | https://www.protocols.io/view/mas-iso-seq-from-10x-single-cell-gene-expression-l-b3duqi6w | Aziz Al'Khafaji | TITLE: MAS-ISO-seq - from 10x Single Cell Gene Expression Libraries
AUTHORS: Aziz Al'Khafaji
[DESCRIPTION]
Method for MAS-ISO-seq from 10x Single Cell Gene Expression Libraries.
[STEPS]
2. WTA amplification:
Set up the following reactions on ice
For 5' libraries:
For 3' libraries:
3. Reaction cleanup and... | ["WTA amplification:\n\nSet up the following reactions on ice\n\nFor 5' libraries:\n \n\nFor 3' libraries:", "Reaction cleanup and quantification\n\n0.8x SPRIselect cleanup - 80 µL beads in 100 µL PCR reaction from step 2.\nElute in 46 µL low-TE\nQubit quantification", "TSO artifact removal\n\n\nTransfer 10 μL (100 μg)... |
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