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 |
|---|---|---|---|---|---|---|---|
21,329 | Yale - Total Cholesterol | null | dx.doi.org/10.17504/protocols.io.y3rfym6 | null | John Stack, Gary Cline | TITLE: Yale - Total Cholesterol
AUTHORS: John Stack, Gary Cline
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Procedure used to determine the total concentration of cholesterol present in blood, serum, and plasma. Ch... | ["Calibrate Cobas for Total Cholesterol analysis by running a multi analyte standard and two control serum.", "Sample handling as performed by Cobas Mira Plus. a) Pipette 3 µL of sample into a cuvette slot. b) Add 275 µL of Cholesterol Rapid Liquid Reagent. c) Mixture is incubated at 37ºC for 10 minutes. d... |
40,205 | CITE-seq for PBMCs | 4 | dx.doi.org/10.17504/protocols.io.bjhmkj46 | https://www.protocols.io/view/cite-seq-for-pbmcs-bjhmkj46 | Nicola Wilson, Fernando Calero-Nieto, Javier Rodríguez-Ubreva, Bertie Gottgens, Esteban Ballestar, Roser Vento-Tormo | TITLE: CITE-seq for PBMCs
AUTHORS: Nicola Wilson, Fernando Calero-Nieto, Javier Rodríguez-Ubreva, Bertie Gottgens, Esteban Ballestar, Roser Vento-Tormo
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a protocol for CITE-seq for PBMCs. It includes the steps for Thawing samples and Antibody St... | ["[Thawing Samples]\nWarm up 10x the volume of thawing medium (RPMI + 10% FBS).", "[Thawing Samples]\nThaw frozen PBMCs in .\n[water bath]", "[Thawing Samples]\nTransfer sample into a 15 ml tube.", "[Thawing Samples]\nAdd 10x volume of thawing medium dropwise into tube.", "[Thawing Samples]\nSpray down with 70% EtOH.",... |
36,101 | Subdiaphragmatic Vagotomy | null | dx.doi.org/10.17504/protocols.io.bfhdjj26 | https://www.protocols.io/view/subdiaphragmatic-vagotomy-bfhdjj26 | Kavi Rude, Jessica Sladek, Colin Reardon | TITLE: Subdiaphragmatic Vagotomy
AUTHORS: Kavi Rude, Jessica Sladek, Colin Reardon
[STEPS]
?. [Anesthesia Induction and Surgical Preparation of the Mouse]
Place the mouse into the induction chamber chamber and slide the lid all the way closed. Turn the appropriate stopcock valves to deliver the appropriate amount of i... | ["[Anesthesia Induction and Surgical Preparation of the Mouse]\nPlace the mouse into the induction chamber chamber and slide the lid all the way closed. Turn the appropriate stopcock valves to deliver the appropriate amount of isoflurane and O2.", "[Anesthesia Induction and Surgical Preparation of the Mouse]\nAs the mo... |
76,132 | Forebrain neural progenitor cells (fbNPCs) differentiation from hiPSCs (dual SMAD inhibition) | 1 | dx.doi.org/10.17504/protocols.io.kxygx9ozzg8j/v1 | https://www.protocols.io/view/forebrain-neural-progenitor-cells-fbnpcs-different-cnkcvcsw | anita.adami | TITLE: Forebrain neural progenitor cells (fbNPCs) differentiation from hiPSCs (dual SMAD inhibition)
AUTHORS: anita.adami
[DESCRIPTION]
This protocol described how to differentiate hiPSCs to forebrain neural progenitor cells using dual SMAD inhibition
[STEPS]
SECTION: hiPSCs dissociation
1. Human induced pluripotent ... | ["[hiPSCs dissociation] Human induced pluripotent stem cells (hiPSCs) are rinsed once with DPBS (GIBCO) and dissociated when 70-90% confluent with 0.5 mM EDTA (75 ml/cm2; GIBCO) at 37 °C for 7 min", "[hiPSCs dissociation] Dissociated cells are then carefully washed away from the wells and collected in wash medium (9.5 ... |
51,877 | Scaled Moderate Throughput Multichannel PhIP Protocol | 1 | null | https://www.protocols.io/view/scaled-moderate-throughput-multichannel-phip-proto-bwwdpfa6 | Sabrina A Mann, Sara Vazquez, Lillian M Khan, Jayant Rajan, Caleigh Mandel-Brehm, Joseph Derisi | TITLE: Scaled Moderate Throughput Multichannel PhIP Protocol
AUTHORS: Sabrina A Mann, Sara Vazquez, Lillian M Khan, Jayant Rajan, Caleigh Mandel-Brehm, Joseph Derisi
[DESCRIPTION]
This protocol was developed as a semi-high throughput technique to perform phage display immunopreceipitation. Here we describe all th... | ["[Day 1- Blocking Plates] Make blocking solution to prevent sample and library from binding to plates. This step also helps with movement of protein A/G beads later on. \n\n Blocking solution (make fresh for every experiment) :\n 3.0% BSA Fraction V\n 1x TBS-Tween\n Mix thorough... |
41,140 | ELISA for quantification of IL-41 in human serum or plasma. | 6 | dx.doi.org/10.17504/protocols.io.bkeuktew | https://www.protocols.io/view/elisa-for-quantification-of-il-41-in-human-serum-bkeuktew | Angel Justiz-Vaillant | TITLE: ELISA for quantification of IL-41 in human serum or plasma.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many ... | ["An anti-human IL-41 coating antibody is adsorbed onto the microwells by incubation overnight at 4°C with carbonate-bicarbonate buffer.", "Add 50 µl of human serum. Human IL-41 present in the serum sample binds to antibodies adsorbed into the microwells.", "The microplate is blocked with 3% non-fat milk-PBS buffer and... |
51,271 | Higienização/esterilização de actígrafos - ActTrust - V.1 | 5 | dx.doi.org/10.17504/protocols.io.bwbfpajn | https://www.protocols.io/view/higieniza-o-esteriliza-o-de-act-grafos-acttrust-v-bwbfpajn | Daniel Vartanian | TITLE: Higienização/esterilização de actígrafos - ActTrust - V.1
AUTHORS: Daniel Vartanian
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Este protocolo faz parte do processo de coleta de dados actigráficos do Grupo Interdisciplinar de Pesquisa em Sono (GIPSO). Ele foi desenhado para os actíg... | ["[Trello]\nAdicione o cartão da tarefa no quadro de trabalho do seu projeto (somente para projetos que usam Kanban)\nAbra o quadro de trabalho de seu projeto e adicione um cartão chamado Realizar a higienização/esterilização de actígrafos na lista Em andamento. Ao clicar sobre o cartão, vá em Etiquetas e selecione (ou... |
24,378 | slant_tilt_demo | null | dx.doi.org/10.17504/protocols.io.322gqge | null | Monica Li | TITLE: slant_tilt_demo
AUTHORS: Monica Li
[STEPS]
?. [Main]
Get the writing data from a digital tablet as attached.
?. Download the data and the command in script, save them in the same folder
?. Run the command | ["[Main]\nGet the writing data from a digital tablet as attached.", "Download the data and the command in script, save them in the same folder", "Run the command"] |
51,054 | Chemically Competent Cell Preparation [Calcium Chloride Method] | 4 | dx.doi.org/10.17504/protocols.io.261ge4k8dv47/v1 | https://www.protocols.io/view/chemically-competent-cell-preparation-calcium-chlo-bv4nn8ve | Harry Akligoh, Jenny Molloy | TITLE: Chemically Competent Cell Preparation [Calcium Chloride Method]
AUTHORS: Harry Akligoh, Jenny Molloy
[DESCRIPTION]
This protocol is a low-cost approach for preparing competent cells using 0.1M CaCl2 solution which is useful in cases where commercial competent cells are unaffordable, it is challenging to recei... | ["[Overnight plating of E. coli] Plate an innoculum of Escherichia coli (e.g. BL21(DE3), JM109) glycerol stock on LB agar without antibiotics.", "[Overnight culture] Pick and transfer a discrete single colony of E. coli into 10 ml LB broth using a sterile innoculation loop or toothpick.", "[Harvesting cells and Washin... |
79,273 | Extraction and ONT MinION Library Preparation of uHMW gDNA | 4 | dx.doi.org/10.17504/protocols.io.j8nlkww11l5r/v4 | https://www.protocols.io/view/extraction-and-ont-minion-library-preparation-of-u-crnhv5b6 | Kaylee S. Herzog, jfauver | TITLE: Extraction and ONT MinION Library Preparation of uHMW gDNA
AUTHORS: Kaylee S. Herzog, jfauver
[DESCRIPTION]
This custom protocol optimizes extraction, purification, and Oxford Nanopore Technologies (ONT) MinION library preparation for ultra-high molecular weight genomic DNA (uHMW gDNA) from parasitic nematodes.... | ["[Part 1: Ultra-HWM gDNA extraction | Zymo Quick-DNA HWM MagBead Plus Kit | ~3 hr] Set dry bath to 55 °C", "For each sample, add the following to a clean 1.5 mL microcentrifuge tube to create a master mix:\n 95 µL \n 95 µL \n 10 µL", "Vortex the master mix gently to mix, then spin down and keep ... |
54,716 | Hydra collecting for citizen scientists | 1 | dx.doi.org/10.17504/protocols.io.bzn4p5gw | https://www.protocols.io/view/hydra-collecting-for-citizen-scientists-bzn4p5gw | Callen Hyland, Kimberly Sladek | TITLE: Hydra collecting for citizen scientists
AUTHORS: Callen Hyland, Kimberly Sladek
[DESCRIPTION]
The freshwater cnidarian Hydra has been a model system for regeneration and developmental biology for over 250 years, but much remains unknown about their biodiversity and global distribution. As a citizen scientist, ... | ["[Collecting Hydra] Gather your materials:\nNotebook and pen\nWhite or clear plastic container (a medium-sized food storage container is ideal)\nGlass Pasteur pipette + rubber bulb\nScrew-cap vials (either glass or plastic)\nMagnifying glass, high powered reading glasses, or headband magnifier\nOptional: plastic tooth... |
14,540 | Determination of phenolic compounds | null | dx.doi.org/10.17504/protocols.io.sfkebkw | null | Jorge Carlos Ruiz Ruiz | TITLE: Determination of phenolic compounds
AUTHORS: Jorge Carlos Ruiz Ruiz
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Phenolic compounds determined using the Folin-Ciocalteu reagent.</div></div>
[STEPS]
?. An aliquot of sample (0.25 mL) was mixed with 0.15 mL of the Folin-Ciocalteu reagent and... | ["An aliquot of sample (0.25 mL) was mixed with 0.15 mL of the Folin-Ciocalteu reagent and 1 mL of a 15% sodium carbonate solution.", "Distilled water was added to a final volume of 2.5 mL. Following incubation for 3 min at 37 °C in a water bath, the absorbance was measured at 750 nm. Gallic acid (Sigma-Aldrich) was us... |
81,457 | 10x Protocols: Visium Fresh Frozen Library Construction -- University of Minnesota TMCs (CG000239 Rev F) | 1 | dx.doi.org/10.17504/protocols.io.81wgby341vpk/v1 | https://www.protocols.io/view/10x-protocols-visium-fresh-frozen-library-construc-ctsrwnd6 | 10x Genomics, Laura J Niedernhofer, David A Bernlohr | TITLE: 10x Protocols: Visium Fresh Frozen Library Construction -- University of Minnesota TMCs (CG000239 Rev F)
AUTHORS: 10x Genomics, Laura J Niedernhofer, David A Bernlohr
[DESCRIPTION]
Protocols from 10x Genomics for Visium Spatial Gene Expression on Fresh Frozen / OCT samples.
Completed without CytAssist componen... | ["10x protocol CG000239, Rev F (Library construction):", "Additional Protocols/Guidelines\n CG000241, Rev D\n CG000240, Rev D\nhttps://www.10xgenomics.com/support/spatial-gene-expression-fresh-frozen"] |
55,362 | Intracellular recordings and post hoc immunofluorescence | 1 | dx.doi.org/10.17504/protocols.io.e6nvwkp97vmk/v1 | https://www.protocols.io/view/intracellular-recordings-and-post-hoc-immunofluor-b2baqaie | Rachel M Gwynne, Katerina Koussoulas, Joel Bornstein | TITLE: Intracellular recordings and post hoc immunofluorescence
AUTHORS: Rachel M Gwynne, Katerina Koussoulas, Joel Bornstein
[DESCRIPTION]
The following protocol was submitted on behalf of the authors from the Bornstein lab by the SPARC project.
This protocol describes methods for standard intracellular recordin... | ["[Electrophysiology] Sacrifice mice by cervical dislocation.", "[Electrophysiology] Open the abdominal cavity using a midline incision and remove the colon.", "[Electrophysiology] To minimize the contractions of the muscle layers during intracellular recordings place the colon in oxygenated [95% O2, 5% CO2] physiologi... |
36,470 | Lipid profile of regular kratom (Mitragyna speciosa Korth.) users in the community setting | 1 | dx.doi.org/10.17504/protocols.io.bfuwjnxe | https://www.protocols.io/view/lipid-profile-of-regular-kratom-mitragyna-speciosa-bfuwjnxe | Mohammad Farris Iman Leong Bin Abdullah, Kok Leng Tan, Salbiah Mohd Isa, Nur Sabrina Yusoff, Nelson Jeng Yeou Chear, Darshan Singh | TITLE: Lipid profile of regular kratom (Mitragyna speciosa Korth.) users in the community setting
AUTHORS: Mohammad Farris Iman Leong Bin Abdullah, Kok Leng Tan, Salbiah Mohd Isa, Nur Sabrina Yusoff, Nelson Jeng Yeou Chear, Darshan Singh
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The protocol d... | ["[Fasting lipid profile and liver function test]\nAll participants were told to begin fasting at 21:00 and then arrive at the Advanced Medical and Dental Institute (AMDI), USM at 09:00 the following day for blood collection (i.e., 12 hours of fasting).", "[Fasting lipid profile and liver function test]\nA blood sample... |
null | null | null | dx.doi.org/10.17504/protocols.io.f27bqhn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><em>This</em> s<em>ampling protocol is designed to collect two fractions: cell pellets and cell-free filtered supernatants. The cell pellets are used for gene expression analyses by RNA-Seq and proteomics. The cell-free fraction is used for analysis of dissolved analytes (e.g... | [] |
86,359 | Iris Classification | 1 | null | https://www.protocols.io/view/iris-classification-cyjxxupn | Ziyong Ma | TITLE: Iris Classification
AUTHORS: Ziyong Ma
[DESCRIPTION]
It is a simple guide for iris classification
[STEPS]
SECTION: Running Iris Classification Project
1. Access the capsule for this project at https://codeocean.com/capsule/0923404/tree.
This project is to build different models to identify different species of... | ["[Running Iris Classification Project] Access the capsule for this project at https://codeocean.com/capsule/0923404/tree.\nThis project is to build different models to identify different species of flowers.", "[Running Iris Classification Project] The data which are images of iris are stored in the images files of dat... |
99,886 | Isolation of Nuclei from Adult Human Brain Tissue for 10x Genomics Platform | 1 | dx.doi.org/10.17504/protocols.io.yxmvmkerng3p/v3 | https://www.protocols.io/view/isolation-of-nuclei-from-adult-human-brain-tissue-ddsn26de | Allen Institute for Brain Science | TITLE: Isolation of Nuclei from Adult Human Brain Tissue for 10x Genomics Platform
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
Isolation of nuclei from frozen adult human brain tissue or thawed and microdissected brain tissue sections for RNA-seq analysis.
Note: Research reported in this publication was... | [] |
87,512 | ASAP protocol: Crystallization of Enterovirus A71 3C protease (PDB code 8CNY) | 1 | dx.doi.org/10.17504/protocols.io.yxmvm3e89l3p/v1 | https://www.protocols.io/view/asap-protocol-crystallization-of-enterovirus-a71-3-czpyx5pw | ryan.lithgo, Peter Marples, daren.fearon, Lizbé Koekemoer | TITLE: ASAP protocol: Crystallization of Enterovirus A71 3C protease (PDB code 8CNY)
AUTHORS: ryan.lithgo, Peter Marples, daren.fearon, Lizbé Koekemoer
[DESCRIPTION]
The crystallization protocol and buffer conditions used to obtain Enterovirus A71 3C protease crystals. The crystal structure was depostited to RCSB PDB ... | ["[Crystallization experiment] Protein and buffer requirements:\n43.2 µL1 millimolar (mM) \n2.88 mL", "[Crystallization experiment] Dispense 30 µL into SwissCI 3 lens plate reservoir wells using a 100 µl multi-channel pipette.\nDispense 150 nL1 millimolar (mM) to each lens using the SPT mosquito.\nDispense 150 nL to ... |
26,110 | Arabidopsis growth medium with varying sulfur and nitrogen content | null | dx.doi.org/10.17504/protocols.io.5q6g5ze | null | Meike Burow | TITLE: Arabidopsis growth medium with varying sulfur and nitrogen content
AUTHORS: Meike Burow
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Media receipe to grow A. thaliana seedlings on plates. </div><div class = "text-block">Variaiton in S and N concentrations.</div></div>
[STEPS]
?. [for 1 L ... | ["[for 1 L medium]\nAB1General media recipeVolume2Minor salts (100x)10 mL3Major salts (10x)100 mL4Ferrous solution (100x)10 mL5Vitamin mix (1000x, Murashige and Skoog, Prod. No. M0409.0100, Duchefa Biochemie)1 mL67water to 1L8adjust pH to 5.8 with 1M KOH9divide 1L to 2x 500 mL (into 1L bottles)10add 4g agar per 5... |
null | null | null | dx.doi.org/10.17504/protocols.io.vbye2pw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol is intended to help you use HOBO data loggers and HOBOware software.
[STEPS]
SECTION: HOBOware
?.
SECTION: Connection
?.
SECTION: HOBOware Basic functions
?.
SECTION: HOBO data logger Programing
?.
SECTION: HOBO data logger Reading and Data export
?. | ["[HOBOware] {\"blocks\":[{\"key\":\"8kkc4\",\"text\":\"Open the HOBOware software (FREE download)\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[],\"data\":[]},{\"key\":\"9dojd\",\"text\":\" \",\"type\":\"atomic\",\"depth\":0,\"inlineStyleRanges\":[],\"entityRanges\":[{\"offset\":0,\"le... |
82,996 | Evaluation of the APUEC package: Alcohol prevention in urgent and emergency care | 1 | dx.doi.org/10.17504/protocols.io.bp2l6xkn1lqe/v1 | https://www.protocols.click/view/evaluation-of-the-apuec-package-alcohol-prevention-cvauw2ew | Holly Blake, Frank Coffey | TITLE: Evaluation of the APUEC package: Alcohol prevention in urgent and emergency care
AUTHORS: Holly Blake, Frank Coffey
[DESCRIPTION]
The aim of the study is to identify the current alcohol prevention practices of staff working in urgent and emergency care settings (UEC) and to explore the views of healthcare profe... | ["[Evaluation of the APUEC package: Alcohol prevention in urgent and emergency care] Evaluation of the APUEC package:\nAlcohol prevention in urgent and emergency care\nVersion 1.0\n18.01.22\nShort title:APUEC Study\nSponsor:University of Nottingham\nSponsor reference:FMHS 415-1121\nFunding Source: Nottingham University... |
66,228 | Set Up Biodata Resource Inventory in Google Colab | 5 | null | https://www.protocols.io/view/set-up-biodata-resource-inventory-in-google-colab-ccwusxew | Kenneth Schackart | TITLE: Set Up Biodata Resource Inventory in Google Colab
AUTHORS: Kenneth Schackart
[DESCRIPTION]
This protocol will guide you on how to get everything in place to update the Biodata Resource Inventory.
This protocol describes how to setup Google Colab, connect your Google Drive, and clone the repository.
Some of t... | ["[Prepare Google Drive] In your Google Drive home directory, create a new folder called GitHub.\n\nInside the GitHub folder, create another folder called biodata_resource_inventory.", "[Connect Colab to Drive] Go to Google Colab.\n\nIf you need to change the account you are using, close the pop up by clicking Cancel a... |
14,402 | Stable transformation of Nicotiana benthamiana | null | dx.doi.org/10.17504/protocols.io.sbaeaie | null | Jana Ordon, Hannelore Espenhahn, Carola Kretschmer, Johannes Stuttmann | TITLE: Stable transformation of Nicotiana benthamiana
AUTHORS: Jana Ordon, Hannelore Espenhahn, Carola Kretschmer, Johannes Stuttmann
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Detailed protocol with pictures for the transformation of </span><span style = "font-style:italic;">Nicotiana be... | ["[Preparation of Agrobacterium suspension]\nStreak the Agrobacterium tumefaciens (A. tumefaciens; GV3101 pMP90) strain carrying the transformation construct on YEB plates containing required antibiotics (Rifampicin, Gentamycin + construct-specific antibiotic). Two days prior to transformation: Inoculate 5 ml YEB liqui... |
98,090 | Human Dorsal Root Ganglion spatial ATAC-seq protocol | 0 | dx.doi.org/10.17504/protocols.io.36wgqn5n5gk5/v1 | https://www.protocols.io/view/human-dorsal-root-ganglion-spatial-atac-seq-protoc-db2i2qce | Úrzula Franco-Enzástiga, Theodore Price | TITLE: Human Dorsal Root Ganglion spatial ATAC-seq protocol
AUTHORS: Úrzula Franco-Enzástiga, Theodore Price
[DESCRIPTION]
In this protocol, we describe how to perform spatial ATAC-seq on fresh-frozen human dorsal root ganglion.
[BEFORE_START]
Required PPE: All work must be done wearing appropriate PPE including lab... | ["[Tissue harversting and storage] Surgically excised lumbar L4 or L5 human dorsal root ganglia (hDRGs) are obtained from organ donors at Southwest Transplant Alliance (STA) at 2 h post cross-clamp.", "[Tissue harversting and storage] Right after dissection, tissue is fresh frozen on powdered dry ice and stored at -80 ... |
94,755 | Real-time PCR bacterial DNA detection | 4 | dx.doi.org/10.17504/protocols.io.q26g7ped8gwz/v1 | https://www.protocols.io/view/real-time-pcr-bacterial-dna-detection-c8sbzwan | Rita Macedo | TITLE: Real-time PCR bacterial DNA detection
AUTHORS: Rita Macedo
[DESCRIPTION]
The identification of bacterial species through molecular techniques is faster and more accurate than phenotypic identification. Analysis of the 16S rRNA gene can potentially be applied to identify a large number of bacteria. The use of un... | ["[Reagent preparation] Rehydrate the primers with ultra-pure water free of DNAses and RNAses to obtain a concentration of 100uM. Make a 1/5 dilution to achieve a working concentration of 20uM. Prepare aliquots according to the working volume and freeze at -20°C.", "The kit is stored at -15°C to -25°C and is stable unt... |
45,511 | Low throughput protocol for immunoprecipitation followed by mass spectrometry of cells stably expressing an HA-tagged protein | 4 | dx.doi.org/10.17504/protocols.io.bqpfmvjn | https://www.protocols.io/view/low-throughput-protocol-for-immunoprecipitation-fo-bqpfmvjn | Harper JW | TITLE: Low throughput protocol for immunoprecipitation followed by mass spectrometry of cells stably expressing an HA-tagged protein
AUTHORS: Harper JW
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Analysis of protein complexes by mass spectrometry provides a powerful approach for identifying p... | ["[Cell Harvest]\nWash plates 2x with cold PBS, then add per plate.\n[ PBS]", "[Cell Harvest]\nGently pipette up and down to dislodge cells and homogenize or gently scrape.", "[Cell Harvest]\nTransfer to 15 mL conical tube and pellet cells , discard sup.\nCentrifuge: 3000 33, 5 min", "[Cell Harvest]\nAdd and transfe... |
20,887 | Cortisol and adrenal androgens as independent predictors of mortality in septic patients_protocol | null | dx.doi.org/10.17504/protocols.io.ymxfu7n | null | Rocío De Castro, David Ruiz, Bernardo-Alio Lavín, Jose Ángel Lamsfus, Luis Vázquez, Coral Montalban, Gilberto Marcano, Raquel Sarabia, María Paz, Cristina Blanco, Miguel Santibáñez | TITLE: Cortisol and adrenal androgens as independent predictors of mortality in septic patients_protocol
AUTHORS: Rocío De Castro, David Ruiz, Bernardo-Alio Lavín, Jose Ángel Lamsfus, Luis Vázquez, Coral Montalban, Gilberto Marcano, Raquel Sarabia, María Paz, Cristina Blanco, Miguel Santibáñez
[DESCRIPTION]
<div class... | ["The collection of blood samples was performed in all cases between 8:00 a.m. and 9:00 a.m.", "Patients did not ingest any food in the previous 10 hours.", "Blood samples were then collected in silicone-vacuum tubes with a silica gel filter without anticoagulant to obtain serum, as well as a venous extraction syringe ... |
51,352 | Well Log Digitization - Recommended Practice | 5 | dx.doi.org/10.17504/protocols.io.bwdypa7w | https://www.protocols.io/view/well-log-digitization-recommended-practice-bwdypa7w | Patrick Walston | TITLE: Well Log Digitization - Recommended Practice
AUTHORS: Patrick Walston
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">An outline of recommended practices for Well Log Digitization.</div></div>
[STEPS]
?. [Minimum Standards]
Environmental ControlWell logs existing on paper or film need to be ... | ["[Minimum Standards]\nEnvironmental ControlWell logs existing on paper or film need to be preserved for future access and should be stored in a controlled environment. The environment that logs are housed and used should be dry and clean, allowing for unfolding of the log to search for areas that need repair without r... |
48,190 | Peptostreptococcal protein L and a Chimeric Protein-LAG sandwich ELISA | 1 | dx.doi.org/10.17504/protocols.io.bta6nihe | https://www.protocols.io/view/peptostreptococcal-protein-l-and-a-chimeric-protei-bta6nihe | Angel Justiz-Vaillant | TITLE: Peptostreptococcal protein L and a Chimeric Protein-LAG sandwich ELISA
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This ELISA was used to study the interactions between Peptostreptococcal protein-L (SpL) and protein LAG (PLAG) with different immunoglobulin ... | ["This ELISA was used to study the interactions between Peptostreptococcal protein-L (SpL) and protein LAG (PLAG) with different immunoglobulin preparations from mammalian and avian species. The 96 well microtiter plate was coated overnight at 4°C with 2 µg/µl per well of SpL in carbonate-bicarbonate buffer pH 9.6.", "... |
90,230 | Evercode Fixation v2.0.2 | 4 | dx.doi.org/10.17504/protocols.io.261ged28jv47/v1 | https://www.protocols.io/view/evercode-fixation-v2-0-2-c4cwysxe | Elisabeth Rebboah, Parse Biosciences | TITLE: Evercode Fixation v2.0.2
AUTHORS: Elisabeth Rebboah, Parse Biosciences
[DESCRIPTION]
This protocol is designed for fixing single cell or single nucleus suspensions for the Parse Biosciences Evercode WT / WT Mega snRNA-seq, "Split-seq".
[BEFORE_START]
For additional questions not discussed below, please contact... | ["[Section 1: Cell fixation] Cell Fixation Setup\nThis protocol is designed for fixing single cell suspensions which will be prepared in step 1.2.1. \n\nNote: If you are fixing nuclei, proceed to the Nuclei Fixation Protocol.", "[Section 1: Cell fixation] (Optional) To maximize cell retention, prepare two BSA coated 15... |
55,493 | Mouse Pancreas Dissection and Fixation for Cryosectioning | 1 | dx.doi.org/10.17504/protocols.io.b2fdqbi6 | https://www.protocols.io/view/mouse-pancreas-dissection-and-fixation-for-cryosec-b2fdqbi6 | Islet and Pancreas Analysis Core | TITLE: Mouse Pancreas Dissection and Fixation for Cryosectioning
AUTHORS: Islet and Pancreas Analysis Core
[DESCRIPTION]
This SOP defines the method used by the Vanderbilt Diabetes Center Islet and Pancreas Analysis (IPA) Core for fixation and embedding of mouse pancreas.
[STEPS]
SECTION: Reagent preparation
1. Keta... | ["[Reagent preparation] Ketamine (15 mg/mL)/xylazine (3 mg/mL) working solution – Use 5 mL syringes with 18G needles. Label all bottles with additive, mix date, and expiration date of earliest-expiring ingredient.", "[Pancreas Dissection and Fixation]", "[Pancreas Dissection and Fixation]", "[Reagent preparation] Pull ... |
57,768 | Small Object and Artefact Photography - 'SOAP' Protocol V.2 | 5 | dx.doi.org/10.17504/protocols.io.b4ngqvbw | https://www.protocols.io/view/small-object-and-artefact-photography-39-soap-39-p-b4ngqvbw | Jacopo Niccolo Cerasoni, Felipe Do Nascimento Rodrigues | TITLE: Small Object and Artefact Photography - 'SOAP' Protocol V.2
AUTHORS: Jacopo Niccolo Cerasoni, Felipe Do Nascimento Rodrigues
[DESCRIPTION]
Photography is among one of the most widely used methods in scientific publications to efficiently and objectively communicate morphological, technological and aes... | ["[Collect Equipment] Collect and prepare equipment (see materials section for full list of equipment).", "[Setting Photographic Environment] Select lens (ideally macro lens), lock camera on a tripod, camera mount or copy stand and place on light box (if available). Ideally use a macro lens.\n\nPlease note that the cam... |
null | null | null | dx.doi.org/10.17504/protocols.io.eyjbfun | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Identifying <em>putative</em> viral sequences from SPAdes-assembled data from the <a href="https://github.com/MicroB3-IS/osd-analysis" target="_blank">Ocean Sampling Day (2014)</a> metagenomic datasets using VirSorter.
[BEFORE_START]
To run this protocol, users must first <a hr... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.cd2s8d | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Please see the Addgene website for additional details.
[STEPS]
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null | null | null | dx.doi.org/10.17504/protocols.io.qisduee | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div>
<div>
<div>
<p>During this step, you will be assembling the ARMS units from the individual parts. The unit is a stack of alternating open layers and closed layers. The closed layers contain a cross-shaped structure dividing the ARMS in four compartments, providing 'cave-li... | [] |
41,037 | Indirect Enzyme Linked Immunosorbent Assay (ELISA) for Detection of Anti-HIV Antibodies in Human Serum | 4 | dx.doi.org/10.17504/protocols.io.bkbmksk6 | https://www.protocols.io/view/indirect-enzyme-linked-immunosorbent-assay-elisa-bkbmksk6 | Angel Justiz-Vaillant, Norma McFarlane-Anderson | TITLE: Indirect Enzyme Linked Immunosorbent Assay (ELISA) for Detection of Anti-HIV Antibodies in Human Serum
AUTHORS: Angel Justiz-Vaillant, Norma McFarlane-Anderson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol was already used successfully to detect anti-HIV antibody in the seru... | ["The 96 well polystyrene microplate (U-shaped bottom; Sigma-Aldrich) is coated with 50 ng of a mixture of synthetic peptides (including the fragment 579-601 of the HIV gp41 and fragments 254-274, 308-331 and 421-438 of the HIV gp120) for 4 h at 37ºC.", "The microplate is blocked with 3% non-fat milk in PBS, 25 µl/well... |
70,171 | CUT&RUN with Drosophila tissues-9-17 | 1 | null | https://www.protocols.io/view/cut-amp-run-with-drosophila-tissues-9-17-cgr3tv8n | lilyli | TITLE: CUT&RUN with Drosophila tissues-9-17
AUTHORS: lilyli
[DESCRIPTION]
We have modified the Cleavage Under Targets and Release Using Nuclease (CUT&RUN) method for epigenomic profiling of histone modifications and chromatin proteins to use dissected Drosophila tissues. In CUT&RUN, cells or tissues are permeabili... | ["[Prepare solutions and beads] Prepare a fresh 5% digitonin solution as follows:\n \n\nWeigh out 50 mg digitonin powder in a 2 ml microcentrifuge tube. Boil some water in a small beaker in a microwave oven, and pipette in and out to warm the 1000 μL pipette tip. Pipette the hot water into the tube with the digitonin p... |
null | null | null | dx.doi.org/10.17504/protocols.io.ekdbcs6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Version February 14th, 2012
[STEPS]
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106,119 | JAX-Sen: Mice selection criteria | 0 | dx.doi.org/10.17504/protocols.io.4r3l2q17pl1y/v1 | https://www.protocols.io/view/jax-sen-mice-selection-criteria-djvf4n3n | Ramalakshmi Ramasamy, Juliana Alcoforado Diniz, Jessica Garofalo, Patrick Fleming, Paul Robson | TITLE: JAX-Sen: Mice selection criteria
AUTHORS: Ramalakshmi Ramasamy, Juliana Alcoforado Diniz, Jessica Garofalo, Patrick Fleming, Paul Robson
[DESCRIPTION]
We aim to select 12 mice (C57BL/6), 6 male and 6 female at 6 and 12 months of age, 3 mice in each age and sex group.
[STEPS] | [] |
77,640 | Equidyn application tutorial | 1 | dx.doi.org/10.17504/protocols.io.5qpvor26xv4o/v1 | https://www.protocols.io/view/equidyn-application-tutorial-cp3gvqjw | Paola Janeiro Valenciano, Luis Augusto Teixeira | TITLE: Equidyn application tutorial
AUTHORS: Paola Janeiro Valenciano, Luis Augusto Teixeira
[DESCRIPTION]
The Equidyn application was developed to evaluate dynamic balance through smartphone-based trunk accelerometry. The evaluation protocol had as main characteristic a reduced support base while having standardized ... | ["The purpose\n\nThe Equidyn application was developed to evaluate dynamic balance through smartphone-based trunk accelerometry. The purpose of the Equidyn application is to guide the assessment of dynamic body balance in a series of probing tasks while measuring trunk accelerometry as an index of body balance stabilit... |
61,027 | HuBMAP | VU TMC Eye/Pancreas | Human Pancreas Processing for Multiple Applications | 1 | dx.doi.org/10.17504/protocols.io.eq2lyp5nelx9/v2 | https://www.protocols.io/view/hubmap-vu-tmc-eye-pancreas-human-pancreas-processi-b7ubrnsn | Diane Saunders, Rita Bottino, Marcela Brissova, Angela Kruse, Jamie Allen, Carrie Romer, Danielle Gutierrez, Jeff Spraggins, Alvin C. Powers | TITLE: HuBMAP | VU TMC Eye/Pancreas | Human Pancreas Processing for Multiple Applications
AUTHORS: Diane Saunders, Rita Bottino, Marcela Brissova, Angela Kruse, Jamie Allen, Carrie Romer, Danielle Gutierrez, Jeff Spraggins, Alvin C. Powers
[DESCRIPTION]
This protocol describes the workflow for collecting huma... | ["[Organ Dissection and Cross-Sectioning] Dissect the pancreas by carefully removing duodenum, mesentery, fat, and spleen (Figure 1).\n\n\n \n\n⚠ Note: If time and personnel permit and there are pieces of duodenum and/or spleen, retain and freeze as tissue blocks (see Flash Freezing subheading below).", "[Organ Disse... |
107,759 | FL-BEEHIV HIV-1 Genotyping and Drug Resistance by Next Generation Sequencing-High throughput extraction | 4 | dx.doi.org/10.17504/protocols.io.n92ld8x3ov5b/v1 | https://www.protocols.io/view/fl-beehiv-hiv-1-genotyping-and-drug-resistance-by-dmgp43vn | Brenna M McGruder Rawson, Jason Blanton | TITLE: FL-BEEHIV HIV-1 Genotyping and Drug Resistance by Next Generation Sequencing-High throughput extraction
AUTHORS: Brenna M McGruder Rawson, Jason Blanton
[DESCRIPTION]
The Florida Department of Health's Bureau of Public Health Laboratories in Jacksonville is developing a protocol for the Next Generation Sequenci... | ["[RNA Extraction] Extract RNA using the Thermofisher MagMAX Viral and Pathogen(MVP) Nucleic Acid Isolation Kit I or MVPII using the Kingfisher Flex\n- The difference is that the MVPI is Reasearch Use Only (RUO) and the MVPII is In Vitro Diagnostic (IVD) approved\n-Both kits are the same, however the MVPI kit is able t... |
65,196 | QGP-1 cell line maintenance protocol | 1 | dx.doi.org/10.17504/protocols.io.bp2l61e1rvqe/v1 | https://www.protocols.io/view/qgp-1-cell-line-maintenance-protocol-cbwkspcw | bellampalli.shreya | TITLE: QGP-1 cell line maintenance protocol
AUTHORS: bellampalli.shreya
[DESCRIPTION]
QGP-1 cell line maintenance protocol; thawing and passaging QGP-1 cells
[STEPS]
SECTION: Thawing protocol
1. Warm media
SECTION: Thawing protocol
2. Swirl cells in 37 degree water bath until vial is thawed
SECTION: Thawing prot... | ["[Thawing protocol] Warm media", "[Thawing protocol] Swirl cells in 37 degree water bath until vial is thawed", "[Thawing protocol] Add 7 mL of culture media to a T25 flask and gently pipette thawed cells into flask", "[Thawing protocol] Let cells adhere for 24 hours and replace half of the culture media with fresh me... |
69,179 | RT-QuIC alpha-synuclein | 1 | null | https://www.protocols.io/view/rt-quic-alpha-synuclein-cfs3tngn | maria.xylaki | TITLE: RT-QuIC alpha-synuclein
AUTHORS: maria.xylaki
[DESCRIPTION]
This protocol is for the detection of prionoid alpha-synuclein forms in human cerebrospinal fluid using the Real Time Quacking-Induced Conversion method (RT-QuIC). The protocol is adapted from Marco J. Russo, Christina D. Orru, Luis Concha‑Marambio, S... | ["[Preparation of Reaction buffer] Reaction mixture is prepared calculating 200 μl per well with the following final concentrations:\n0.3 mg/mL recombinant alpha-synuclein\n0.5 M NaCl\n100 mM PIPES buffer\n5 μM ThT", "[Bead preparation] Beads are blocked with 1% BSA in 100mM PIPES for 1 hr and washed twice with PIPES."... |
43,631 | Rearing Ambrosia Beetles in Media | 3 | dx.doi.org/10.17504/protocols.io.bnupmevn | https://www.protocols.io/view/rearing-ambrosia-beetles-in-media-bnupmevn | James Skelton, Sawyer Adams, Andrew J. Johnson | TITLE: Rearing Ambrosia Beetles in Media
AUTHORS: James Skelton, Sawyer Adams, Andrew J. Johnson
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The purpose of this protocol is to produce a supply of living beetles in various developmental stages in the laboratory. </div><div class = "text-block"><s... | [] |
61,919 | https://www.jpost.com/promocontent/keto-extreme-fat-burner-south-africa-price-at-clicks-dischem-denmark-living-lifestyle-705766 | 3 | dx.doi.org/10.17504/protocols.io.4r3l2o33xv1y/v1 | https://www.protocols.io/view/https-www-jpost-com-promocontent-keto-extreme-fat-b8p7rvrn | ketoextremefatburnerCOST | TITLE: https://www.jpost.com/promocontent/keto-extreme-fat-burner-south-africa-price-at-clicks-dischem-denmark-living-lifestyle-705766
AUTHORS: ketoextremefatburnerCOST
[DESCRIPTION]
Keto Extreme Fat Burner requires some genuine festival now and can be bought without a doubt in the least demanding ever way.
[STEPS] | [] |
101,922 | Sensor Guided Needle Entry Procedures: A Scoping Review of Advancements to the Veress Needle & Selected Needle Entry Techniques | 0 | dx.doi.org/10.17504/protocols.io.bp2l621jkgqe/v2 | https://www.protocols.io/view/sensor-guided-needle-entry-procedures-a-scoping-re-dfsa3nae | Chimwemwe Miti, Richard Scott, Hermes Gadelha-Bloomfield | TITLE: Sensor Guided Needle Entry Procedures: A Scoping Review of Advancements to the Veress Needle & Selected Needle Entry Techniques
AUTHORS: Chimwemwe Miti, Richard Scott, Hermes Gadelha-Bloomfield
[DESCRIPTION]
Primary entry during minimally invasive abdominal surgery remains the one step associated with contr... | ["[Eligibility Criteria] Studies in English", "[Eligibility Criteria] Publication period 1992- May 2024", "[Eligibility Criteria] Articles with full text available", "[Eligibility Criteria] Human subjects"] |
91,508 | Gewebesammlung Frischgewebe Zystektomie | 1 | null | https://www.protocols.io/view/gewebesammlung-frischgewebe-zystektomie-c5kuy4ww | Annika Fendler, Bettina Ergün | TITLE: Gewebesammlung Frischgewebe Zystektomie
AUTHORS: Annika Fendler, Bettina Ergün
[DESCRIPTION]
Dieses Protokoll beschreibt die Schritte für die Sammlung von Frischgewebe, Gefriergewebe (Fresh-frozen), und Blut von Patienten mit Harnblasenkarzinom nach Zystektomie.
Verwandte Dokumente:
Protokoll zur Blutaufarb... | ["[Aufarbeitung im Labor] weiter mit Protokoll:", "[Gewebesammlung im Schnellschnitt] Nach Rückmeldung des Schnellschnitts geht eine Person zur Gewebeentnahme. \nTüte Blase und Stickstoffbehälter mitnehmen.\nArbeitsanleitung (siehe Abbildung) beachten.", "[Gewebesammlung im Schnellschnitt] 4x 15 ml Falcons mit 10,2 ml... |
45,992 | The calculation of gut metabolic modules from gene profile | 1 | dx.doi.org/10.17504/protocols.io.bq6gmzbw | https://www.protocols.io/view/the-calculation-of-gut-metabolic-modules-from-gene-bq6gmzbw | Qi Wang | TITLE: The calculation of gut metabolic modules from gene profile
AUTHORS: Qi Wang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The calculation of gut metabolic modules from gene profile</div></div>
[STEPS]
?. Step 1: the putative amino acid sequences were translated from the gene catalogues and... | ["Step 1: the putative amino acid sequences were translated from the gene catalogues and aligned against the proteins/domains in the KEGG databases (release 79.0, with animal and plant genes removed) using BLASTP (v2.2.26, default parameter except that -e 0.01 -b 100 -K 1 -F T -m 8). Each protein was assigned to the KO... |
55,856 | FLASH-seq protocol (V1) | 4 | dx.doi.org/10.17504/protocols.io.b2sqqedw | https://www.protocols.io/view/flash-seq-protocol-v1-b2sqqedw | Simone Picelli, Vincent Hahaut | TITLE: FLASH-seq protocol (V1)
AUTHORS: Simone Picelli, Vincent Hahaut
[DESCRIPTION]
The single-cell RNA-sequencing (scRNA-seq) field has evolved tremendously since the first paper was published back in 2009. While the first methods analysed just a handful of cells, the throughput and performance rapidly increased ... | ["[Prepare lysis mix] Prepare the following lysis mix:\n ReagentReaction concentrationVolume (µl)384-well plateTriton-X100 (10% v/v)0.2%0.0208.448dNTP mix (25 mM each)6 mM0.240101.376SMART dT30VN (100 µM)1.8 mM0.0187.603RNAse inhibitor (40 U/µL)1.2 U/µL0.03012.672DTT (100 mM)1.2 mM0.0125.069FS TSO (100 µM)9.2 µM0.09... |
74,339 | QIAGEN DNeasy PowerSoil Kit | 4 | dx.doi.org/10.17504/protocols.io.n2bvj8drpgk5/v1 | https://www.protocols.io/view/qiagen-dneasy-powersoil-kit-ckubuwsn | QIAGEN | TITLE: QIAGEN DNeasy PowerSoil Kit
AUTHORS: QIAGEN
[DESCRIPTION]
For the isolation of microbial genomic DNA from all soil types
The DNeasy PowerSoil Kit comprises a novel and proprietary method for isolating genomic DNA from environmental samples using patented Inhibitor Removal Technology® (IRT). This kit is intende... | ["[Sample preparation & cell lysis] ADD 0.25 g of soil sample to the PowerBead Tube \n\nVORTEX gently to mix", "[Sample preparation & cell lysis] ADD 60 µL of Solution C1 \n\nINVERT several times or vortex briefly", "[Sample preparation & cell lysis] SECURE PowerBead Tubes horizontally using a Vortex Adapte... |
44,006 | Vivarium Population Spenser: Emigration protocol | 5 | dx.doi.org/10.17504/protocols.io.bn8emhte | https://www.protocols.io/view/vivarium-population-spenser-emigration-protocol-bn8emhte | Camila Rangel Smith, Kasra Hosseini | TITLE: Vivarium Population Spenser: Emigration protocol
AUTHORS: Camila Rangel Smith, Kasra Hosseini
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Description of the steps followed by Vivarium Population Spenser library when running the Emigration module. </div></div>
[STEPS]
?. For each time ste... | ["For each time step:", "Divide the annual international emigration rates for that local authority by the number of time steps existing in a year.", "Select all individuals in the sample that appear as \"alive\" and have an associated gender.", "For these individuals, get the emigration rate given their age, gender, et... |
70,259 | A reproducibility protocol and dataset on the biomedical sentence similarity | 5 | dx.doi.org/10.17504/protocols.io.36wgq429xvk5/v4 | https://www.protocols.io/view/a-reproducibility-protocol-and-dataset-on-the-biom-cguttwwn | Alicia Lara Clares, Juan J. Lastra-Díaz, Ana Garcia-Serrano | TITLE: A reproducibility protocol and dataset on the biomedical sentence similarity
AUTHORS: Alicia Lara Clares, Juan J. Lastra-Díaz, Ana Garcia-Serrano
[DESCRIPTION]
This protocol introduces a set of reproducibility resources with the aim of allowing the exact replication of the experiments introduced by our main pap... | ["[Installing Docker on Ubuntu] If Docker is not installed in your machine, instructions below install latest version of Docker CE. For further details, we refer the reader to the official Docker setup page https://docs.docker.com/install/linux/docker-ce/ubuntu/\n\nFirst, we update the system:\n \nWe install the depend... |
87,597 | Basic Cell Culture Maintenance: Splitting Cells | 1 | null | https://www.protocols.io/view/basic-cell-culture-maintenance-splitting-cells-czsmx6c6 | leroi.bwh | TITLE: Basic Cell Culture Maintenance: Splitting Cells
AUTHORS: leroi.bwh
[DESCRIPTION]
Basic protocol to split THP1
[BEFORE_START]
Make complete DMEM:
Reagent Volume DMEM 432.5 mL FBS 50 mL Pen/Strep 5 mL HEPES (1M, pH 7.4) 12.5 mL
[STEPS]
SECTION: Preparation
1. Confirm that cells are at least 80... | ["[Preparation] Confirm that cells are at least 80% confluent by microscopy.", "[Remove Media] Aspirate the media from the flask using a sterile autoclaved glass pipette. Do not touch the cells with the pipette.", "[Transfer] Transfer ALL contents/cells to a 50 mL falcon tube.", "[Spin] Spin down 130 rcf for 7 minutes.... |
null | null | null | dx.doi.org/10.17504/protocols.io.qg8dtzw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>we generated five clonal, axenic strains of Symbiodinium. These strains were assigned to clades A (two strains), B, E, and F based on their chloroplast 23S rDNA</p>
<p>sequences. Growth studies in liquid cultures showed that the clade B strain and one of the clade A strains w... | [] |
36,593 | Isolation and identification of cancer stem cells by ALDH activity assay | null | dx.doi.org/10.17504/protocols.io.bfyrjpv6 | https://www.protocols.io/view/isolation-and-identification-of-cancer-stem-cells-bfyrjpv6 | Kwangok P Nickel, Austin M. Maas, Andrea Pennati, Randall Kimple | TITLE: Isolation and identification of cancer stem cells by ALDH activity assay
AUTHORS: Kwangok P Nickel, Austin M. Maas, Andrea Pennati, Randall Kimple
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Cancer stem cells (CSCs) are a small subpopulation of tumor cells that are thought to be respons... | ["Prepare activated ALDEFLUOR assay reagent, Bodipy-aminoacetaldehyde (BAAA), according to the manufacturer’s directions. Make aliquots and store them at .Note: In this example, a head and neck cancer cell line, UM-SCC47 , is analyzed. The experimental approach can be used to study cells isolated from primary human ... |
null | null | null | dx.doi.org/10.17504/protocols.io.j7icrke | null | null | TITLE: No Title
AUTHORS:
[STEPS] | [] |
107,209 | Stereotaxic Injection by Iontophoresis | 1 | dx.doi.org/10.17504/protocols.io.14egn8ewzg5d/v5 | https://www.protocols.io/view/stereotaxic-injection-by-iontophoresis-dkxh4xj6 | Allen Institute for Brain Science | TITLE: Stereotaxic Injection by Iontophoresis
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
This protocol describes the delivery of a neuronal tracer using the iontophoretic method. The surgery uses a stereotaxic system to target specific brain coordinates in the mouse.
Note: Research reported in this pu... | [] |
26,293 | TRANSDUCTION OF i3NEURONS (Support Protocol 4) | null | dx.doi.org/10.17504/protocols.io.5wvg7e6 | null | Michael S. Fernandopulle, Ryan Prestil, Christopher Grunseich, Chao Wang, Li Gan, Michael E. Ward | TITLE: TRANSDUCTION OF i3NEURONS (Support Protocol 4)
AUTHORS: Michael S. Fernandopulle, Ryan Prestil, Christopher Grunseich, Chao Wang, Li Gan, Michael E. Ward
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Lentiviral infection of neurons can be used for a variety of applications in microscopy and... | ["[Day 0]\nCoat a 6-well dish with PLO (see Basic Protocol 6).", "[Day 1]\nCheck cells for confluency under an inverted microscope. Cells should be > 95 % confluent for maximal viral production efficiency\nIf necessary, wait a day to transfect so that the cells are nearly confluent.", "[Day 0]\nPlate 2.5 × 106 Lenti-X ... |
75,099 | LEGACY01: ASSESSMENT AND FOLLOW-UP | 1 | null | https://www.protocols.io/view/legacy01-assessment-and-follow-up-cmj3u4qn | Katrina M Pollock, Calliope Dendrou | TITLE: LEGACY01: ASSESSMENT AND FOLLOW-UP
AUTHORS: Katrina M Pollock, Calliope Dendrou
[DESCRIPTION]
This protocol details assessment and follow-up in an experimental medicine study of seasonal influenza vaccination responses in Lymph nodE single-cell Genomics in AnCestrY (LEGACY01).
[GUIDELINES]
ASSESSMENT AND FOLLO... | [] |
44,727 | stLFR library construction | 4 | dx.doi.org/10.17504/protocols.io.bpwxmpfn | https://www.protocols.io/view/stlfr-library-construction-bpwxmpfn | Chunhua Li, Xianwei Yang, Libin Shao, Rui Zhang, QunLiu, Mengqi Zhang, Shanshan Liu, Shanshan Pan, Weizhen Xue, Congyan Wang, Chunyan Mao, He Zhang, Guangyi Fan | TITLE: stLFR library construction
AUTHORS: Chunhua Li, Xianwei Yang, Libin Shao, Rui Zhang, QunLiu, Mengqi Zhang, Shanshan Liu, Shanshan Pan, Weizhen Xue, Congyan Wang, Chunyan Mao, He Zhang, Guangyi Fan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used to clarity the process of ... | ["Sample preparationRemove the long-fragment gDNA from and store on ice.\n4 °C", "Transposon Insertion", "Transfer long-fragment gDNA gently into a 0.2ml PCR tube. Without mixing, add Nuclease Free Water to a total volume of . Collect and dispense long fragment DNA slowly (the process should take >) each time when pi... |
63,429 | Steve Harvey CBD Gummies THE MOST POPULAR CBD GUMMY BEARS IN UNITED STATES READ HERE REVIEWS, BENEFITS, SIDE EFFECT, INGREDIENTS, DOES IT REALLY WORK? IS IT SAFE? BUY NOW GET INSTANTLY | 1 | dx.doi.org/10.17504/protocols.io.8epv59m14g1b/v1 | https://www.protocols.io/view/steve-harvey-cbd-gummies-the-most-popular-cbd-gumm-b97dr9i6 | asns | TITLE: Steve Harvey CBD Gummies THE MOST POPULAR CBD GUMMY BEARS IN UNITED STATES READ HERE REVIEWS, BENEFITS, SIDE EFFECT, INGREDIENTS, DOES IT REALLY WORK? IS IT SAFE? BUY NOW GET INSTANTLY
AUTHORS: asns
[DESCRIPTION]
Steve Harvey CBD Gummies
[STEPS]
1. Steve Harvey CBD Gummies
➢Product Name —Steve Harvey CB... | ["Steve Harvey CBD Gummies\n\n \n\n➢Product Name —Steve Harvey CBD Gummies Reviews\n➢Main Benefits—Improve Metabolism & Help in Pain Relief\n➢Composition —NaturalOrganic Compound\n➢Side-Effects—NA\n➢Rating :—⭐⭐⭐⭐⭐\n➢Availability —Online\n➢Price (for Sale) Buy Now Here —Click Here\nSteve Harvey CBD Gummies - You plan to... |
52,673 | CeVICA selection protocol | 4 | dx.doi.org/10.17504/protocols.io.bxn9pmh6 | https://www.protocols.io/view/cevica-selection-protocol-bxn9pmh6 | Xun Chen, Matteo Gentili, Nir Hacohen, Aviv Regev | TITLE: CeVICA selection protocol
AUTHORS: Xun Chen, Matteo Gentili, Nir Hacohen, Aviv Regev
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The step-by-step protocol for performing the experimental steps of CeVICA, a cell-free nanobody selection platform. This protocol describes one round of select... | ["Coat 100 µl Protein G magnetic beads with 4 µl anti-Flag antibody (diluted in 250 µl PBST) at room temperature for 1hour (see the manufacturer’s protocol for more detail).", "Wash antibody coated beads once with PBST. Then resuspend beads in PBST and aliquot equally into two tubes. One tube for pre-clearing, one tube... |
null | null | null | dx.doi.org/10.17504/protocols.io.ghhbt36 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is our transfer protocol for the transfer of proteins using the Trans-Blot Turbo Transfer system from Bio-Rad. We use it with our single gel we have made based the One-Gel system by Ahn T et al (2001) (DOI:<a href="https://dx.doi.org/10.1006/abio.2001.5038" target="_blan... | [] |
37,747 | Miltenyi Buffer | 3 | null | https://www.protocols.io/view/miltenyi-buffer-bg4tjywn | Marco Cosentino, Elisa Storelli, Alessandra Luini, Emanuela Rasini, Massimiliano Legnaro, Marco Ferrari, Franca Marino | TITLE: Miltenyi Buffer
AUTHORS: Marco Cosentino, Elisa Storelli, Alessandra Luini, Emanuela Rasini, Massimiliano Legnaro, Marco Ferrari, Franca Marino
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This recipe is used in the following protocol:</div><div class = "text-block"><span style = "font-wei... | [] |
70,872 | PD-L1 expression as predictor of immunotherapy eligibility in penile squamous cell carcinoma patients | 1 | dx.doi.org/10.17504/protocols.io.bp2l69b4klqe/v1 | https://www.protocols.io/view/pd-l1-expression-as-predictor-of-immunotherapy-eli-chfyt3pw | Muhammad Haritsyah Warli, Fauriski Febrian Prapiska, Ginanda Putra Siregar, Bungaran Sihombing, Syah Mirsya Warli | TITLE: PD-L1 expression as predictor of immunotherapy eligibility in penile squamous cell carcinoma patients
AUTHORS: Muhammad Haritsyah Warli, Fauriski Febrian Prapiska, Ginanda Putra Siregar, Bungaran Sihombing, Syah Mirsya Warli
[DESCRIPTION]
We investigated the correlation between PD-L1 expression and poor prognos... | ["[PD-L1 Antibody Preparation] Reagent used to stain PD-L1 in this IHC staining was MD21R clone (Medaysis CA), ready to use (rabbit PD-L1 antibody)", "[Pretreatment] Pretreatment was done with EDTA pH8.0, 15 minutes using a Pressure Cooker\n\n15 min \nOR\n\n60 min 95 °C to 99 °C", "The detection was done by using post ... |
83,151 | Create Mask for Axonal Quantification Analysis with FIJI | 1 | dx.doi.org/10.17504/protocols.io.14egn3b9yl5d/v1 | https://www.protocols.click/view/create-mask-for-axonal-quantification-analysis-wit-cvfpw3mn | Oscar Moreno Ramos, Elizabeth P. | TITLE: Create Mask for Axonal Quantification Analysis with FIJI
AUTHORS: Oscar Moreno Ramos, Elizabeth P.
[DESCRIPTION]
This is a protocol describing how to create a quantified mask from an image of fluorescence-tagged axonal projections using FIJI/ImageJ software.
[STEPS]
1. Upload TIFF image of single-channel fluor... | ["Upload TIFF image of single-channel fluorescent axons to Fiji", "Adjust brightness/contrast (keyboard shortcut: ctrl + shift + C)", "Select Plugins -> Analyze -> Tubeness", "Enter 0.5 for the sigma value", "Synchronize windows: select Analyze -> Tools -> Synchronize windows", "Open thresholding (shortcut: ctrl + shif... |
30,048 | Herbarium Specimens | null | dx.doi.org/10.17504/protocols.io.9j8h4rw | null | Sabine St-Jean | TITLE: Herbarium Specimens
AUTHORS: Sabine St-Jean
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Here we describe the standardised protocol used by the </span><a href="http://www.caboscience.org/" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">Canadian Airb... | ["[Specimen Collection]\nCreate the plant record in Fulcrum.", "[Specimen Collection]\nIn Fulcrum, under Plants ⟶ Metadata, select the appropriate project (see Open Vegetation Survey Protocol → Guidelines → Site Specific Infos).", "[Specimen Collection]\nUnder Plants ⟶ Site and Plot, select the appropriate site (see Op... |
null | null | null | dx.doi.org/10.17504/protocols.io.hatb2en | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The protocol can be used to create and extrude phospholipid liposomes. This extrusion protocol roughly follows <a href="https://avantilipids.com/divisions/equipment/mini-extruder-extrusion-technique/" target="_blank">some guidelines published by the manufacturer</a>. However,... | [] |
108,111 | QuPath Visualization/Segmentation | 4 | dx.doi.org/10.17504/protocols.io.dm6gp35d5vzp/v2 | https://www.protocols.io/view/qupath-visualization-segmentation-dmtp46mn | Michael X. Henderson | TITLE: QuPath Visualization/Segmentation
AUTHORS: Michael X. Henderson
[DESCRIPTION]
This protocol describes QuPath visualization/segmentation.
[GUIDELINES]
QuPath is a visualization and segmentation platform optimized for whole slide images. This the place where you can visualize all your slides, and create the outp... | ["[QuPath Visualization/Segmentation] Open QuPath. Click “Create Project.”", "[QuPath Visualization/Segmentation] Select your QuPath folder for this project and upload images by pressing “Add Images.” Navigate to full slide scans and add slides for this project.", "[QuPath Visualization/Segmentation] Upload series of i... |
21,229 | Vandy - Tail-Cuff Blood Pressure | null | dx.doi.org/10.17504/protocols.io.yymfxu6 | null | Chee Lim | TITLE: Vandy - Tail-Cuff Blood Pressure
AUTHORS: Chee Lim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">The tail-cuff blood pressure measurement is a non-invasive test and the principle is the same as that of the infl... | ["Turn on the BP-2000 computer and control unit and set the heating platform at approximately 34ºC.", "Place a mouse in the magnetic restraining device on the platform leaving its tail free.", "Insert and slide the mouse tail all the way through the corresponding tail-cuff and tape the tail down.", "Place the LED light... |
62,536 | Keto Complete France: Ingrédients 100% naturels Commandez en ligne ! | 1 | dx.doi.org/10.17504/protocols.io.yxmvmn5zbg3p/v1 | https://www.protocols.io/view/keto-complete-france-ingr-dients-100-naturels-comm-b9bgr2jw | sgfzjkoza | TITLE: Keto Complete France: Ingrédients 100% naturels Commandez en ligne !
AUTHORS: sgfzjkoza
[DESCRIPTION]
Keto Complete France Echec aux faits. Ce n'est pas facile! Keto Complete Cela est connu depuis un moment Keto Complete France, mais les gens ne restent pas assis là comme des hippy-dippy pour faire le travail... | [] |
51,390 | Cell culture, transfection, and imaging | 1 | dx.doi.org/10.17504/protocols.io.36wgq41j3vk5/v1 | https://www.protocols.io/view/cell-culture-transfection-and-imaging-bwe6pbhe | Will Hancock-Cerutti, Pietro De Camilli | TITLE: Cell culture, transfection, and imaging
AUTHORS: Will Hancock-Cerutti, Pietro De Camilli
[DESCRIPTION]
This protocol describes general procedures for culturing HeLa cells, transient transfection, and imaging using an Andor Dragonfly spinning disk confocal system.
[STEPS]
SECTION: General preparation
1. Culture... | ["[General preparation] Culture the HeLa-M cells at 37 °C in 5% CO2 and DMEM containing 10% FBS, 100 U/ml penicillin, 100 mg/mL streptomycin, and 2 Milimolar (mM) L-glutamine (all from Gibco).", "[General preparation] For live-cell imaging experiments, seed the cells on glass-bottomed dishes (MatTek) at a concentration... |
null | null | null | dx.doi.org/10.17504/protocols.io.e95bh86 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>TAP medium is the most widely used for growth of the green alga <em>Chlamydomonas reinhardtii</em>. Note the presence of acetate effects the photosynthetic ability of the alga and minimal medium should be used instead if quantifying effects of mutations or inhibitors on photo... | [] |
97,505 | Protocol for Nuclei Isolation and Automated 10X Genomics Single Cell 5' Gene Expression for Human Ovary Explants | 0 | dx.doi.org/10.17504/protocols.io.8epv5r6x5g1b/v1 | https://www.protocols.io/view/protocol-for-nuclei-isolation-and-automated-10x-ge-dbf92jr6 | Nicolas Martin | TITLE: Protocol for Nuclei Isolation and Automated 10X Genomics Single Cell 5' Gene Expression for Human Ovary Explants
AUTHORS: Nicolas Martin
[DESCRIPTION]
This is the 10X Genomics Automated Single Cell 5' Gene Expression protocol using nuclei suspension isolated from fresh frozen human ovary explants. The Chro... | ["[Nuclei Isolation Protocol for Human Ovary Explants] Chapter 1—Single Cell Gene Expression & Chromium Fixed RNA Profiling of the protocol CG000505 REV A was used to isolate nuclei from frozen human ovary explants with the following modifications: 1) a cordless motor pestle (VWR, Catalog number 47747-370) was used for... |
null | null | null | dx.doi.org/10.17504/protocols.io.fapbidn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Provides a short introduction of using the MEGAHIT, IDBA-UD, and SPAdes assemblers.</p>
[GUIDELINES]
<p><img id="s-mce-img" class="s-mce-img" src="https://s3.amazonaws.com/pr-journal/d9vc2w6.png" data-src="https://s3.amazonaws.com/pr-journal/d9vc2w6.png" data-ofn="Screen Sho... | [] |
95,184 | Building a phenotype-o-mat: A low-cost DIY plate reader for high-throughput phenotype measurements | 1 | dx.doi.org/10.17504/protocols.io.yxmvm3r3ol3p/v1 | https://www.protocols.io/view/building-a-phenotype-o-mat-a-low-cost-diy-plate-re-c87qzzmw | Ben Braverman | TITLE: Building a phenotype-o-mat: A low-cost DIY plate reader for high-throughput phenotype measurements
AUTHORS: Ben Braverman
[DESCRIPTION]
We've developed a DIY, low-cost, 96-well plate imager called the phenotype-o-mat. This protocol outlines the steps to assemble it yourself. We cover:
1) 3D-printing compone... | ["[3D-printing components] The phenotype-o-mat has the following 3D-printed components:\nPlate-holder base\nCamera arm\nCamera mount\nCircular filter slider\nLED ring and diffuser mount clip\nLED diffuser ring\nArduino Nano Every case (credit: leondl on Thingiverse)\n\nAccess STL files for these parts >", "[3D-printing... |
89,256 | Immunofluorescence for confocal imaging | 4 | dx.doi.org/10.17504/protocols.io.kxygx3nrkg8j/v1 | https://www.protocols.io/view/immunofluorescence-for-confocal-imaging-c3egyjbw | Cecilia Tubert | TITLE: Immunofluorescence for confocal imaging
AUTHORS: Cecilia Tubert
[DESCRIPTION]
This protocol describes the steps for tissue preparation for immunostaining and confocal images aquisition. It also describes the steps for immunostaining and confocal imaging.
[STEPS]
SECTION: Perfusion and fixation - Before the pr... | ["[Perfusion and fixation - Before the procedure:] Under the hood, pour PBS and PFA solutions in 50ml tubes.", "[Perfusion and fixation - Before the procedure:] Attach the perfusion needle to the connector at the end of the tubing", "[Perfusion and fixation - Before the procedure:] Start running PBS through the tubing.... |
70,494 | High molecular weight plant DNA extraction for PacBio HiFi sequencing | 4 | dx.doi.org/10.17504/protocols.io.x54v9dm7pg3e/v1 | https://www.protocols.io/view/high-molecular-weight-plant-dna-extraction-for-pac-cg36tyre | Kanae Nishii, Michael Möller, Robert G. Foster, Laura L. Forrest, Nathan Kelso, Sadie Barber, Caroline Howard, Michelle L. Hart | TITLE: High molecular weight plant DNA extraction for PacBio HiFi sequencing
AUTHORS: Kanae Nishii, Michael Möller, Robert G. Foster, Laura L. Forrest, Nathan Kelso, Sadie Barber, Caroline Howard, Michelle L. Hart
[DESCRIPTION]
High molecular weight and high quality DNA is mandatory for successful long-read sequencing... | ["[Before starting DNA extraction] Prepare 400 ml NI buffer in a glass beaker and leave on ice.\non ice", "[Before starting DNA extraction] Prepare 100 ml sorbitol buffer in two 50 ml Falcon tubes.\non ice", "[Before starting DNA extraction] Affix nylon mesh on top of one empty 500 ml glass beaker with string or tape (... |
72,428 | RNA Extraction from Cecum Contents of Gnotobiotic Mice | 4 | dx.doi.org/10.17504/protocols.io.5jyl8jjx7g2w/v1 | https://www.protocols.io/view/rna-extraction-from-cecum-contents-of-gnotobiotic-ciykufuw | Haley Gause | TITLE: RNA Extraction from Cecum Contents of Gnotobiotic Mice
AUTHORS: Haley Gause
[DESCRIPTION]
RNA extraction from the cecum contents of gnotobiotic mice colonized with extremely minimal communities (single yeast and/or single bacterial community) can be difficult due to excess complex carbohydrates. These carbohyd... | ["[At time of euthanization] Harvest cecum and cecum contents. Drop ½ of cecum contents into 10 ml RNAlater. Leaves tubes at 4oC for 1 day minimum (7 day maximum).", "[At time of euthanization] Pre-weigh 2ml tubes. Add 1ml of RNAlater-cecum contents to each tube (~200mg contents) using wide-bore 1000µL tips and centrif... |
null | null | null | dx.doi.org/10.17504/protocols.io.hpcb5iw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
82,960 | Fecal sample pooling for SARS-CoV-2 real-time RT-PCR screening | 1 | dx.doi.org/10.17504/protocols.io.yxmvm3oobl3p/v1 | https://www.protocols.io/view/fecal-sample-pooling-for-sars-cov-2-real-time-rt-p-cu9qwz5w | Leyi Wang, Antonio Leonardi-Cattolica, Sandipty Kayastha, megan.miller | TITLE: Fecal sample pooling for SARS-CoV-2 real-time RT-PCR screening
AUTHORS: Leyi Wang, Antonio Leonardi-Cattolica, Sandipty Kayastha, megan.miller
[DESCRIPTION]
This document includes the information and procedures to do sample pooling for fecal samples and real-time RT-PCR for SARS- CoV-2 using CDC based primers ... | ["[Prepare fecal samples] Add 1 mLphosphate buffered saline (PBS, pH 7.4) to an Eppendorf tube.", "[Prepare fecal samples] Use cotton tipped wooden swabs to wipe a fecal sample in four places.", "[Prepare fecal samples] Place the cotton swab with fecal material into the PBS in the Eppendorf tube.", "[Prepare fecal samp... |
76,090 | Quantitative Flow Cytometry (qFCM) protocols for end-to-end optimization of cross-platform extracellular vesicle studies | 2 | dx.doi.org/10.17504/protocols.io.36wgqjb5ovk5/v1 | https://www.protocols.io/view/quantitative-flow-cytometry-qfcm-protocols-for-end-cni2vcge | Sean M Cook, Vera A Tang, Joanne Lannigan, Jennifer C. Jones, Joshua A Welsh | TITLE: Quantitative Flow Cytometry (qFCM) protocols for end-to-end optimization of cross-platform extracellular vesicle studies
AUTHORS: Sean M Cook, Vera A Tang, Joanne Lannigan, Jennifer C. Jones, Joshua A Welsh
[DESCRIPTION]
Flow cytometry (FCM) is a common extracellular particles (EPs), including viruses and extra... | [] |
67,085 | Synthetic Procedure of Pinoresinol | 6 | dx.doi.org/10.17504/protocols.io.dm6gpbnojlzp/v1 | https://www.protocols.io/view/synthetic-procedure-of-pinoresinol-cdrms546 | Lisa.Stanley, Rui Katahira, Gregg T. Beckham | TITLE: Synthetic Procedure of Pinoresinol
AUTHORS: Lisa.Stanley, Rui Katahira, Gregg T. Beckham
[DESCRIPTION]
A direct understanding of the degradation reaction pathways of lignin polymers in biomass is difficult due to the complexity of lignin’s structure. To overcome the difficulty, simple lignin dimeric and trimeri... | ["[Synthetic Procedure]", "[Synthetic Procedure] Coniferyl alcohol (2.0782 g , 11.5 mmol) was dissolved in acetone (15 mL ) then diluted with deionized (D.I.) water (70 mL ). A solution of iron (III) chloride hexahydrate (3.4289 g , 12.7 mmol, 1.1 eq) in D.I. water (30 mL ) was then added to the reaction mixture. The m... |
33,691 | Drop Dialysis | null | dx.doi.org/10.17504/protocols.io.bc53iy8n | null | Ken Christensen | TITLE: Drop Dialysis
AUTHORS: Ken Christensen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is modified from the Drop Dialysis protocol available at http://www.neb.com.</div><div class = "text-block"><span style = "font-weight:bold;">Introduction</span></div><div class = "text-block"... | ["Pour 30–100 ml of dialysis buffer, usually double-distilled water or 1X TE (10 mM Tris-HCl, 1 mM EDTA, pH 8.0), into a Petri dish or beaker.", "Float a 13mm or 25 mm diameter, Type-VS Millipore membrane (MF type, VS filter, mean pore size = 0.025 μm, Millipore, Inc. #VSWP02500 or #VSWP01300) shiny side up on the dial... |
null | null | null | dx.doi.org/10.17504/protocols.io.tbfeijn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<h1> </h1>
<p>This has been adapted by Kylie James in Dr Sarah Teichmann’s laboratory. Kylie has used this protocol many times for retrieval of lymphocytes from human colon (mLN, sigmoid, caecum and transverse) for 10X chromium genomics. FACS analysis shows a resultant populatio... | [] |
42,238 | B-PER Lysis--CHEM 584 | 4 | dx.doi.org/10.17504/protocols.io.bmg6k3ze | https://www.protocols.io/view/b-per-lysis-chem-584-bmg6k3ze | Ken Christensen | TITLE: B-PER Lysis--CHEM 584
AUTHORS: Ken Christensen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The Thermo Scientific B-PER Bacterial Protein Extraction Reagent enables mild extraction of proteins from bacteria (</span><span style = "font-style:italic;">E. coli</span><span>) without the ... | ["[B-PER Lysis to extract soluble protein]\nPellet bacterial cells by centrifugation at 5000 × g in a tared tube for .", "[B-PER Lysis to extract soluble protein]\nOptional: Add of lysozyme and of DNase I per of B-PER Reagent added.\n2 µl\n2 µl\n1 mL", "[B-PER Lysis to extract soluble protein]\nAdd of B-PER Reagent ... |
94,802 | Spatially variable gene detection | 4 | dx.doi.org/10.17504/protocols.io.rm7vzxp28gx1/v1 | https://www.protocols.io/view/spatially-variable-gene-detection-c8tszwne | Peter Kilfeather | TITLE: Spatially variable gene detection
AUTHORS: Peter Kilfeather
[DESCRIPTION]
Spatially variable gene detection from Kilfeather, Khoo et al., 2024
[STEPS]
SECTION: Protocol
1. Spatially variable genes were identified using SpatialDE2 with default settings. Coordinates and full expression matrices of each brain wer... | ["[Protocol] Spatially variable genes were identified using SpatialDE2 with default settings. Coordinates and full expression matrices of each brain were supplied, divided by cell type. To combine results from separate samples, a meta-analysis was performed on the raw P values from each sample, using Fisher’s method. T... |
32,915 | Dual Optical Mapping of Action Potentials and Calcium Transients in the Mouse Heart during Optogenetic Stimulation of the ICNS | null | dx.doi.org/10.17504/protocols.io.bcdtis6n | null | Pradeep Rajendran, Guy Salama, Ching Zhu, Peter Hanna | TITLE: Dual Optical Mapping of Action Potentials and Calcium Transients in the Mouse Heart during Optogenetic Stimulation of the ICNS
AUTHORS: Pradeep Rajendran, Guy Salama, Ching Zhu, Peter Hanna
[STEPS]
?. The animal is euthanized by a method approved by IACUC (Institutional Animal Care and Use Committee), the chest... | ["The animal is euthanized by a method approved by IACUC (Institutional Animal Care and Use Committee), the chest opened, the heart and lungs removed, and the aorta quickly cannulated on a Langendorff apparatus to perfuse the coronary vessels. The cannulation step should occur in ice-cold Tyrode's solution (112mM NaCl... |
52,298 | Protocol of the competitive audit for designing and developing the National Edition of Aldo Moro's works | 1 | dx.doi.org/10.17504/protocols.io.bxbipike | https://www.protocols.io/view/protocol-of-the-competitive-audit-for-designing-an-bxbipike | Sebastian Barzaghi | TITLE: Protocol of the competitive audit for designing and developing the National Edition of Aldo Moro's works
AUTHORS: Sebastian Barzaghi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left">This work aims to define a series of reference models that woul... | ["[Data collection]\nA sample of 30 editions has been selected for their analysis and evaluation on the basis of certain criteria. The evaluation criteria that have been used to review the sample are based on part of the criteria for reviewing scholarly digital editions compiled by Patrick Sahle in collaboration with G... |
null | null | null | dx.doi.org/10.17504/protocols.io.cy6xzd | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?. | [] |
55,860 | FLASH-seq Low-Amplification protocol (V1) | 4 | dx.doi.org/10.17504/protocols.io.b2suqeew | https://www.protocols.io/view/flash-seq-low-amplification-protocol-v1-b2suqeew | Simone Picelli, Vincent Hahaut | TITLE: FLASH-seq Low-Amplification protocol (V1)
AUTHORS: Simone Picelli, Vincent Hahaut
[DESCRIPTION]
Building upon the existing Smart-seq2/3 workflows, we developed FLASH-seq (FS), a new full-length scRNA-seq method capable of detecting a significantly higher number of genes than both previous versions, requiring... | ["[Prepare lysis mix] Prepare the following lysis mix:\n ReagentReaction concentrationVolume (µl)384-well plateTriton-X100 (10% v/v)0.2%0.0208.448dNTP mix (25 mM each)6 mM0.240101.376SMART dT30VN (100 µM)1.8 mM0.0187.603RNAse inhibitor (40 U/µL)1.2 U/µL0.03012.672DTT (100 mM)1.2 mM0.0125.069FS TSO (100 µM)9.2 µM0.09... |
null | null | null | dx.doi.org/10.17504/protocols.io.kpxcvpn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><strong>ABSTRACT</strong></p>
<p><strong>BACKGROUND: </strong>Transfusion therapy is associated with increased morbidity, mortality and costs. Conventional coagulation tests are weak bleeding predictors, poorly reflecting coagulation in vivo. Thromboelastometry (ROTEM) provid... | [] |
34,844 | Diatom DNA library preparation for Illumina Miseq Sequencing using the rbcL marker gene | 1 | dx.doi.org/10.17504/protocols.io.bd94i98w | https://www.protocols.io/view/diatom-dna-library-preparation-for-illumina-miseq-bd94i98w | Cecile Chardon, Valentin Vasselon, Marine Vautier, Sonia Lacroix, Agnès Bouchez, Frédéric Rimet, Isabelle Domaizon | TITLE: Diatom DNA library preparation for Illumina Miseq Sequencing using the rbcL marker gene
AUTHORS: Cecile Chardon, Valentin Vasselon, Marine Vautier, Sonia Lacroix, Agnès Bouchez, Frédéric Rimet, Isabelle Domaizon
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is part of the DNA... | ["[Primers preparation]\nAt the start of a new DNA library preparation, you must prepare \"fresh\" primers at 10 µM, the volume required to process all the samples and make aliquots to avoid freezing / thawing of primers.", "[Primers preparation]\nGlobal informationsThe original diatom rbcL primers include the Diat_rbc... |
86,211 | TMT labelling | 4 | dx.doi.org/10.17504/protocols.io.n92ldmp69l5b/v1 | https://www.protocols.io/view/tmt-labelling-cyfbxtin | Louise Uoselis | TITLE: TMT labelling
AUTHORS: Louise Uoselis
[DESCRIPTION]
TMT labelling
[STEPS]
1. Reconstitute lyophilised peptides in 25 µL by vortexing each sample for ~10 s, and then leaving to sit at Room temperature for 15 min. Each sample was then sonicated for 5 min in a waterbath sonicator in an ice slurry.
2. Determine ... | ["Reconstitute lyophilised peptides in 25 µL by vortexing each sample for ~10 s, and then leaving to sit at Room temperature for 15 min. Each sample was then sonicated for 5 min in a waterbath sonicator in an ice slurry.", "Determine the peptide concentration of each sample spectroscopically", "Aliquot10 µg of peptides... |
null | null | null | dx.doi.org/10.17504/protocols.io.e7rbhm6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This is a collection of protocols for high quality genomic DNA extraction using the OmniPrep™ kit. Please refer to the appropriate protocol below depending on your application.</p>
[STEPS]
?. | [] |
90,196 | Determining IIDP Minimal Donor Criteria | 1 | dx.doi.org/10.17504/protocols.io.bp2l6xrp1lqe/v1 | https://www.protocols.io/view/determining-iidp-minimal-donor-criteria-c4buysnw | Integrated Islet Distribution Program | TITLE: Determining IIDP Minimal Donor Criteria
AUTHORS: Integrated Islet Distribution Program
[DESCRIPTION]
This SOP defines the pancreas donor profile acceptable for use in the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) sponsored research in the Integrated Islet Distribution Program (IID... | ["[I.\tIIDP Donor Inclusion Criteria] The following are IIDP Inclusion Criteria for Pancreas Donors for Human Islet Isolation:", "[I.\tIIDP Donor Inclusion Criteria] A multi-organ donor or pancreas-only donor if the donor meets all the criteria for multi-organ donation", "[I.\tIIDP Donor Inclusion Criteria] Adequate in... |
79,620 | Preparation of Tissue for Volume Electron Microscopy using Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) | 4 | dx.doi.org/10.17504/protocols.io.kqdg39d97g25/v1 | https://www.protocols.io/view/preparation-of-tissue-for-volume-electron-microsco-crzcv72w | Jillian C Danne, Rachel Templin, Gediminas Gervinskas, Denis Korneev, Sergey Gorelick, Georg Ramm | TITLE: Preparation of Tissue for Volume Electron Microscopy using Focused Ion Beam Scanning Electron Microscopy (FIB-SEM)
AUTHORS: Jillian C Danne, Rachel Templin, Gediminas Gervinskas, Denis Korneev, Sergey Gorelick, Georg Ramm
[DESCRIPTION]
Volume Electron Microscopy (vEM) allows for the three-dimensional imaging of... | ["[Fixation] All fixation and processing steps must be performed in a fume hood wearing appropriate personal protective equipment (PPE). The Material Safety Data Sheet (MSDS) for each chemical must be read before commencing.\n\nDissect out the tissue of interest on a Teflon plate or dental wax sheet using fine forceps ... |
30,340 | Copy of Protocol for the production of crude alcoholic extracts from native plants | null | dx.doi.org/10.17504/protocols.io.9vch62w | null | Marissol Leite, Hadda Tercya Lima Silva, Zanderluce Gomes Luis, Aline Coutinho Cavalcante, Caio Maximino, Diogenes Silva | TITLE: Copy of Protocol for the production of crude alcoholic extracts from native plants
AUTHORS: Marissol Leite, Hadda Tercya Lima Silva, Zanderluce Gomes Luis, Aline Coutinho Cavalcante, Caio Maximino, Diogenes Silva
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes th... | ["Separate the leaves and inflorescences from plants with the help of scissors.", "Rinse the material under running water and then with distilled water to remove debris.", "Dry the material with paper towels to remove the excess of water.", "Grind the leaves and flowers with a knife mill or blender and / or just cut wi... |
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