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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80,140 | CUT&Tag-direct for whole cells with CUTAC | 1 | dx.doi.org/10.17504/protocols.io.x54v9mkmzg3e/v4 | https://www.protocols.io/view/cut-amp-tag-direct-for-whole-cells-with-cutac-cshkwb4w | Steven Henikoff, Jorja Henikoff, Kami Ahmad | TITLE: CUT&Tag-direct for whole cells with CUTAC
AUTHORS: Steven Henikoff, Jorja Henikoff, Kami Ahmad
[DESCRIPTION]
We previously introduced Cleavage Under Targets & Tagmentation (CUT&Tag), an epigenomic profiling method in which antibody tethering of the Tn5 transposase to a chromatin epitope of interest maps... | ["[REAGENT SETUP (for up to 16 samples)] Binding buffer Mix 200 μL 1M HEPES-KOH pH 7.9*, 100 μL 1M KCl, 10 μL 1M CaCl2 and 10 μL 1M MnCl2, and bring the final volume to 10 mL with dH2O. Store the buffer at 4 °C for up to several months. *HEPES-NaOH pH 7.5 is OK.\n\nTriton-Wash buffer Mix 1 mL 1 M HEPES pH 7.5, 1.5 mL 5... |
74,086 | Cost-efficient Yeast genome Flongle library | 4 | dx.doi.org/10.17504/protocols.io.e6nvwjb2wlmk/v1 | https://www.protocols.io/view/cost-efficient-yeast-genome-flongle-library-ckkeuute | Yutaro Hori | TITLE: Cost-efficient Yeast genome Flongle library
AUTHORS: Yutaro Hori
[DESCRIPTION]
A cost-efficient protocol for constructing a Flongle library.
[STEPS]
1. Assemble the following components to end repair and add A to the genomic sample:
Incubate at 20 °C for 5 min, then 65 °C for 5 min.
2. Add 50 µL of Am... | ["Assemble the following components to end repair and add A to the genomic sample:\n\n \nIncubate at 20 °C for 5 min, then 65 °C for 5 min.", "Add 50 µL of Ampure beads (or equivalent beads) and mix well.\nWash with 75 % EtOH twice and elute with 11 µL of 10 millimolar (mM) Tris-HCl (pH 8.0). \nKeep the tube on the... |
58,169 | Vagus Nerve Selective Stimulation and EIT recording | 1 | dx.doi.org/10.17504/protocols.io.b42zqyf6 | https://www.protocols.io/view/vagus-nerve-selective-stimulation-and-eit-recordin-b42zqyf6 | Enrico Ravagli, Svetlana Mastitskaya, Nicole Thompson, Kirill Aristovich, David Holder | TITLE: Vagus Nerve Selective Stimulation and EIT recording
AUTHORS: Enrico Ravagli, Svetlana Mastitskaya, Nicole Thompson, Kirill Aristovich, David Holder
[DESCRIPTION]
This electrophysiology protocol describes the electrical stimulation and measurement steps needed to localize branches and image functional activ... | ["[Preparation] Animal (pig) is anaesthetized (Isofluorane) and cervical vagus is exposed through surgery.", "[Preparation] Clean electrodes of the nerve cuffs by dipping into ethanol and then physiological solution (or saline solution).", "[Preparation] Apply nerve cuffs to exposed cervical left vagus and connect to t... |
null | null | null | dx.doi.org/10.17504/protocols.io.nsadeae | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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55,146 | Pilot Exercise: Generating the Illumina SampleSheet and sharing data via BaseSpace | 1 | dx.doi.org/10.17504/protocols.io.bz4ip8ue | https://www.protocols.io/view/pilot-exercise-generating-the-illumina-samplesheet-bz4ip8ue | Ruth Timme, Maria Balkey, Tunc Kayikcioglu, Candace Bias, Cameron Boerner, James Pettengill | TITLE: Pilot Exercise: Generating the Illumina SampleSheet and sharing data via BaseSpace
AUTHORS: Ruth Timme, Maria Balkey, Tunc Kayikcioglu, Candace Bias, Cameron Boerner, James Pettengill
[DESCRIPTION]
This protocol describes the required steps to generate Illumina SampleSheet and provides guidelines for sharing... | ["[Generating Sequencing SampleSheet] Create your SampleSheet using Excel or a text editor. Name your sample sheet according your internal protocols, and use a *.csv extension. The sample sheet is organized in sections titled Header, Reads, Settings and Data. Section headings are case-sensitive and shown in bracke... |
35,957 | Isolation of natural killer (NK) cells from human blood products | 1 | dx.doi.org/10.17504/protocols.io.81wgbp94yvpk/v1 | https://www.protocols.io/view/isolation-of-natural-killer-nk-cells-from-human-bl-bfcvjiw6 | Philippa R Kennedy | TITLE: Isolation of natural killer (NK) cells from human blood products
AUTHORS: Philippa R Kennedy
[DESCRIPTION]
Standard isolation procedure for peripheral blood mononuclear cells from human blood leukopheresis products
[STEPS]
1. Healthy donor blood products (Leukopaks) were obtained from Memorial Blood Bank (Minn... | ["Healthy donor blood products (Leukopaks) were obtained from Memorial Blood Bank (Minneapolis, MN). All samples were de-identified and their use was approved by the University of Minnesota and NMDP institutional review board in accordance with the Declaration of Helsinki.", "Peripheral blood mononuclear cells (PBMCs) ... |
null | null | null | dx.doi.org/10.17504/protocols.io.f7wbrpe | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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null | null | null | dx.doi.org/10.17504/protocols.io.j9icr4e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The spinal bones of knockout mice were fixed in ethanol, stained by the Villanueva method, and embedded in methyl methacrylate without decalcification. The administration schedule involved a single subcutaneous injection of tetracycline administered to null and wild-type mice... | [] |
62,824 | Methods for Visualization of Pig Vagus Nerve "Vagotopy" Using Ultrasound | 1 | dx.doi.org/10.17504/protocols.io.bp2l61m4zvqe/v1 | https://www.protocols.io/view/methods-for-visualization-of-pig-vagus-nerve-34-va-b9kgr4tw | Megan Settell, Rex Chen, Kip Ludwig | TITLE: Methods for Visualization of Pig Vagus Nerve "Vagotopy" Using Ultrasound
AUTHORS: Megan Settell, Rex Chen, Kip Ludwig
[DESCRIPTION]
This protocol describes the surgical, ultrasound, and histology methods for visualizing pig vagus nerve vagotopy.
[STEPS]
SECTION: Preparing Surgical Pocket for Vagus N... | ["[Preparing Surgical Pocket for Vagus Nerve Ultrasound] Surgically Expose the Vagus Nerve", "[Preparing Surgical Pocket for Vagus Nerve Ultrasound] Place wire under the vagus nerve every 2-3 cm, where histology samples will be taken.", "[Preparing Surgical Pocket for Vagus Nerve Ultrasound] Place subject in dorsal rec... |
38,919 | 1: User-friendly protocol: Probe set design (SABER-FISH) | 1 | null | https://www.protocols.io/view/1-user-friendly-protocol-probe-set-design-saber-fi-bh9fj93n | Jocelyn Y. Kishi, Sylvain W. Lapan, Brian J Beliveau, Emma R. West, Allen Zhu, Hiroshi M. Sasaki, Sinem Saka, Yu Wang, Constance L Cepko, Peng Yin | TITLE: 1: User-friendly protocol: Probe set design (SABER-FISH)
AUTHORS: Jocelyn Y. Kishi, Sylvain W. Lapan, Brian J Beliveau, Emma R. West, Allen Zhu, Hiroshi M. Sasaki, Sinem Saka, Yu Wang, Constance L Cepko, Peng Yin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol offers step by ste... | ["Retrieve BED file for gene or gene region of interset from UCSC genome browser:50\nGenome-wide probe sets have already been generated for a variety of stringency levels. The probe set files with medium probes end in ‘b’, for instance the ‘mm10 chr16b.bed’ file. B stands for ‘balanced.’ Probe sets by chromosome for a ... |
35,899 | NEBExpress Ni Spin Column Reaction Protocol (NEB #S1427) | null | null | https://www.protocols.io/view/nebexpress-ni-spin-column-reaction-protocol-neb-s1-bfa3jign | New England Biolabs | TITLE: NEBExpress Ni Spin Column Reaction Protocol (NEB #S1427)
AUTHORS: New England Biolabs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-style:italic;">Ni resin can be used for the purification of His-tagged fusion proteins under native or denaturing conditions</span></div><... | ["[Buffer Preparation for Ni Spin Columns]\nPrepare buffers for Ni Spin Columns as follows: ABCD1Lysis/Binding Buffer:\n\n20 mM sodium phosphate, \n300 mM NaClWash Buffer:\n\n20 mM sodium phosphate,\n 300 mM NaCl,\n 5 mM ImidazoleElution Buffer:\n\n20 mM sodium phosphate,\n300 mM NaCl,\n500 mM Imidazole22X IMAC Buffe... |
29,107 | Cell-free lysate (E. coli) preparation with sonication | null | dx.doi.org/10.17504/protocols.io.8nthven | https://www.protocols.io/view/cell-free-lysate-e-coli-preparation-with-sonicatio-8nthven | Nadanai Laohakunakorn | TITLE: Cell-free lysate (E. coli) preparation with sonication
AUTHORS: Nadanai Laohakunakorn
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Production of cell-free lysate from E. coli BL21 Star (DE3) with optional induction of T7 RNAP. Adapted from Kwon and Jewett 2015. Features:</div><div class = ... | ["[Bacterial growth]\nPrepare all materials for bacterial cultureThis protocol will make of culture to yield around of lysate with a protein concentration of around 40 - 80 mg/mL.\n200 ml\n1 ml", "[Bacterial growth]\nGrow overnight mini-culture", "[Bacterial growth]\nReconstitute LB media from premix as per instructi... |
99,848 | BAF_Protocol_010 Metabolomics LC-MS(/MS): Vanquish UPLC and Orbitrap ID-X | 0 | dx.doi.org/10.17504/protocols.io.bp2l629ddgqe/v1 | https://www.protocols.io/view/baf-protocol-010-metabolomics-lc-ms-ms-vanquish-up-ddrg253w | Nicholas Sherman | TITLE: BAF_Protocol_010 Metabolomics LC-MS(/MS): Vanquish UPLC and Orbitrap ID-X
AUTHORS: Nicholas Sherman
[DESCRIPTION]
This protocol is the basic LC and MS running parameters for metabolite runs. The samples typically have fewer components (ions) than proteomics so the gradients are shorter and most molecules are si... | ["[Prepare samples for injection] Suspend dried metabolite extracted samples with 100 µL of 0.1% Formic acid in water containing 100X diluted Metabolomics QRESS heavy labeled standards.", "[Prepare samples for injection] Vortex, microfuge for 15 min at max speed, and take off 50 µL into autosampler vial (do not touch... |
48,587 | Sub-ARTIC Illumina SARS-CoV-2 Spike sequencing protocol (LoCost) V3.2 | 1 | dx.doi.org/10.17504/protocols.io.btpjnmkn | https://www.protocols.io/view/sub-artic-illumina-sars-cov-2-spike-sequencing-pro-btpjnmkn | Gavin Horsburgh, Paul Parsons, Kathryn Maher, Steve Paterson, Terry Burke | TITLE: Sub-ARTIC Illumina SARS-CoV-2 Spike sequencing protocol (LoCost) V3.2
AUTHORS: Gavin Horsburgh, Paul Parsons, Kathryn Maher, Steve Paterson, Terry Burke
[DESCRIPTION]
This protocol describes a procedure for sequencing the Spike region of SARS-CoV-2 using short amplicons (146-208bp). The method has proved t... | ["[Multiplex PCR] Primers are separated into two pools, odd and even, depending on where they sit across the Spike region. See the guidelines section for further details. In a clean pre-PCR hood set up two PCR reactions, one per pool as follows:", "[NEBNext Ultra II End Prep] Prepare a master mix of the reagents as bel... |
52,124 | Detecting reactive oxygen species in free-living symbiotic dinoflagellates exposed to nanoparticles | 1 | dx.doi.org/10.17504/protocols.io.bw54pg8w | https://www.protocols.io/view/detecting-reactive-oxygen-species-in-free-living-s-bw54pg8w | Liza M M Roger, Nastassja Lewinski | TITLE: Detecting reactive oxygen species in free-living symbiotic dinoflagellates exposed to nanoparticles
AUTHORS: Liza M M Roger, Nastassja Lewinski
[DESCRIPTION]
2',7'-dichlorodihydrofluorescein diacetate (DCFH-DA) is a popular fluorescent probe for the detection of oxidative stress in cells. Since the probe can b... | ["[Chemicals] - 2',7'-dichlorodihydrofluorescein diacetate (DCFH-DA, Sigma-Aldrich, CAS Number 4091-99-0, MW 487.29, Product Number D6883)\n- Hydrogen peroxide (H2O2, 30%, Sigma-Aldrich, CAS Number 7722-84-1, MW 34.01, Product Number 216763)\n- BD DifcoTM Marine Broth 2216 (dehydrated culture media, Fisher Scientific, ... |
null | null | null | dx.doi.org/10.17504/protocols.io.iaucaew | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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64,357 | @>>> https://pillsfect.com/tenaxtreme-male-enhancement/ | 3 | dx.doi.org/10.17504/protocols.io.81wgb6koqlpk/v1 | https://www.protocols.io/view/gt-gt-gt-https-pillsfect-com-tenaxtreme-male-enha-ca4dsgs6 | H A | TITLE: @>>> https://pillsfect.com/tenaxtreme-male-enhancement/
AUTHORS: H A
[DESCRIPTION]
There are many of these on the Internet, and finding the one they give you the most amount of quality for your money is really not that
[STEPS] | [] |
81,199 | SARS-CoV-2 consensus genome reconstruction, quality control, and lineage analysis | 1 | null | https://www.protocols.io/view/sars-cov-2-consensus-genome-reconstruction-quality-ctipwkdn | Benjamin Schwessinger | TITLE: SARS-CoV-2 consensus genome reconstruction, quality control, and lineage analysis
AUTHORS: Benjamin Schwessinger
[DESCRIPTION]
This protocols is part of the ANU Biosecurity mini-research project #2 "An SARS-COV2 incursion scenario: Genomics, phylogenetics, and incursions." This mini-research project is modeled ... | ["[Section I: Consensus genome reconstruction using Epi2Me and the 'wf-artic'.] This section aims to reconstruct each samples consensus genome based on the publication here https://academic.oup.com/biomethods/article/5/1/bpaa014/5873518?login=true and an adaptation of the artic Sars-CoV-2 analytics workflow h... |
null | null | null | dx.doi.org/10.17504/protocols.io.j8ncrve | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This protocol simplifies current approaches for agar overlay plaque assays by eliminating the use of tubes for premixing of agar, hosts, and viruses, in favor of pipetting each of these directly onto the bottom agar. The benefits of this approach include simplified experimental ... | ["[I. Preparation of the top agar in beaker-waterbath] Prepare a beaker-waterbath: Place bottle of top agar into a glass beaker and add water to the beaker up to the level of the top agar in the bottle; for example, a 500 ml glass bottle into a 1l beaker.", "[I. Preparation of the top agar in beaker-waterbath] {\"block... |
39,267 | SARS-CoV-2 RBD ELISA | 4 | null | https://www.protocols.io/view/sars-cov-2-rbd-elisa-bikbkcsn | Anita Iyer | TITLE: SARS-CoV-2 RBD ELISA
AUTHORS: Anita Iyer
[STEPS]
?. Coating:-Dilute SARS-CoV-2 RBD antigen to 1 µg/mL in carbonate buffer (20 mL per 384 well plate).-Add 50 µl/well of this antigen to a 384 well plate (200µl/ well for 96 well plate).-Cover with plate seal. Using a microcentrifuge, quick spin plates to allow the... | ["Coating:-Dilute SARS-CoV-2 RBD antigen to 1 µg/mL in carbonate buffer (20 mL per 384 well plate).-Add 50 µl/well of this antigen to a 384 well plate (200µl/ well for 96 well plate).-Cover with plate seal. Using a microcentrifuge, quick spin plates to allow the solution to settle at the bottom.-Incubate at room temper... |
54,885 | FPCount protocol - in-lysate (purification free) protocol | 4 | dx.doi.org/10.17504/protocols.io.bzudp6s6 | https://www.protocols.io/view/fpcount-protocol-in-lysate-purification-free-proto-bzudp6s6 | Eszter Csibra, Guy-Bart Stan | TITLE: FPCount protocol - in-lysate (purification free) protocol
AUTHORS: Eszter Csibra, Guy-Bart Stan
[DESCRIPTION]
FPCount is a complete protocol for fluorescent protein calibration, consisting of:
1. FP expression and production of cell lysates.
2. FP concentration determination in a microplate reader.
3. FP ... | ["[Expression] [ Day 1 ]\n\nOvernight culture set-up:\n50ml LB\n50ul cam\n50ul arabinose 0.02%\nglycerol stock scraping of BL21/pS381_ara_His-FP transformant (or equivalent)\n30oC 250rpm\novernight expression…", "[Fractionation] Prep for next stage: prep eppies and cool them for after the spin\n\n[ Day 2 ]\n\nSpin out ... |
100,678 | COI-Gene Metabarcoding Library Prep: Dual-PCR Method | 1 | dx.doi.org/10.17504/protocols.io.261ge5d7yg47/v1 | https://www.protocols.io/view/coi-gene-metabarcoding-library-prep-dual-pcr-metho-deje3cje | rute.carvalho Carvalho, Colleen Kellogg, Matt Lemay | TITLE: COI-Gene Metabarcoding Library Prep: Dual-PCR Method
AUTHORS: rute.carvalho Carvalho, Colleen Kellogg, Matt Lemay
[DESCRIPTION]
This protocol is used for eDNA metabarcoding of the Cytochrome Oxidase I (COI) "Leray fragment", using Pair-End Illumina MiseqSequencing. As part of the Hakai Institute Ocean Observing... | ["[Preparations] Ensure that the laboratory is appropriately configured and that staff has appropriate training. See \"Guidelines\" for more information. Pay attention to the separation of pre and post-PCR spaces and equipment.", "[Triplicate PCR Amplification (1st PCR)] Preparations\n\n \n\n Reagents:\n (Or equal)\n ... |
101,373 | 100ml EB buffer (PH=8) | 0 | null | https://www.protocols.io/view/100ml-eb-buffer-ph-8-de853hy6 | Menglin WANG | TITLE: 100ml EB buffer (PH=8)
AUTHORS: Menglin WANG
[DESCRIPTION]
This is the recipe for how to make 100ml EB buffer (PH=8)
[STEPS]
SECTION: 100ml EB buffer (10mM Tris-HCl) pH=8
1. Prepare 80 mL in a suitable container.
SECTION: 100ml EB buffer (10mM Tris-HCl) pH=8
2. Add 0.12114 g of to the solution.
SEC... | ["[100ml EB buffer (10mM Tris-HCl) pH=8] Prepare 80 mL in a suitable container.", "[100ml EB buffer (10mM Tris-HCl) pH=8] Add 0.12114 g of to the solution.", "[100ml EB buffer (10mM Tris-HCl) pH=8] Adjust solution to desired (pH 8.0) using HCl (typically pH ≈ 7.0).", "[100ml EB buffer (10mM Tris-HCl) pH=8] Ad... |
108,745 | Slide-tags snRNA-seq Protocol (v.1.2 TAGS) | 0 | null | https://www.protocols.io/view/slide-tags-snrna-seq-protocol-v-1-2-tags-dnfh5bj6 | Andrew Russell, Jackson Weir, Naeem Nadaf, Evan Macosko, Fei Chen | TITLE: Slide-tags snRNA-seq Protocol (v.1.2 TAGS)
AUTHORS: Andrew Russell, Jackson Weir, Naeem Nadaf, Evan Macosko, Fei Chen
[DESCRIPTION]
This protocol is for use with TAGS V9 beads, and snRNA-seq profiling of tagged nuclei on the 10x Genomics Chromium Single Cell Gene Expression 3’ v3.1 platform. The extraction buff... | ["[Preparation] Equilibrate the following in the cryostat:\nTissue\nTissue punches\nTweezers\nBrushes\nTissue chuck", "[Preparation] Set a swing-bucket centrifuge that can accommodate 50 mL falcon tubes to 4 ℃.", "[Preparation] Prepare the following buffers and keep on ice: \nDissociation buffer\n\n \n\n\nThis buffer w... |
61,793 | Passaging of cells | 4 | dx.doi.org/10.17504/protocols.io.ewov1n3qkgr2/v1 | https://www.protocols.io/view/passaging-of-cells-b8j9rur6 | Guido Krähenbühl | TITLE: Passaging of cells
AUTHORS: Guido Krähenbühl
[DESCRIPTION]
General Lab procedure, Cell passage
[BEFORE_START]
Warm up culture media, PBS and Trypsin in a 37 °C
[STEPS]
1. Inspect cells for confluency, when 70-90 % confluency is reached cells are ready for passage
2. Discard media and wash once with PBS
3.... | ["Inspect cells for confluency, when 70-90 % confluency is reached cells are ready for passage", "Discard media and wash once with PBS", "Add Trypsin to fully cover the surface of the culture vessel", "Incubate for 5 min at 37 °C", "Lightly tap the culture vessel and check for cell detachement. If cells are still attac... |
67,354 | Using polyan: a Python package for modelling polysome profiles from ribosome density data | 5 | null | https://www.protocols.io/view/using-polyan-a-python-package-for-modelling-polyso-cdz2s78e | Tobias von der Haar | TITLE: Using polyan: a Python package for modelling polysome profiles from ribosome density data
AUTHORS: Tobias von der Haar
[DESCRIPTION]
The assessment of transcriptome-wide ribosome binding to mRNAs is useful for studying the dynamic regulation of protein synthesis in living cells. Two methods frequently applied ... | ["[General Functionality] polyan provides Python functions for modelling polysome profiles from input data on transcript abundance and ribosome occupancy of transcripts. Typically, such data are intended to be the result of ribosome footprinting experiments, but in principle any experimental or computational technique ... |
98,660 | Protocol for metagenomics sampling, storage, and sequencing of human stool | 0 | dx.doi.org/10.17504/protocols.io.yxmvmek36g3p/v1 | https://www.protocols.io/view/protocol-for-metagenomics-sampling-storage-and-seq-dckc2usw | Federica Pinto, Nicola Segata | TITLE: Protocol for metagenomics sampling, storage, and sequencing of human stool
AUTHORS: Federica Pinto, Nicola Segata
[DESCRIPTION]
This SOP provides guidelines for optimal human fecal sample collection and conservation practice with the scope of fecal microbiota characterization by shotgun sequencing.
[STEPS]
SE... | ["[General guidelines for sample processing for shotgun sequencing] The protocols provided below are routinely applied by Prof. Nicola Segata Lab and are based on results by the International Human Microbiome Standards (IHMS) consortium. \n\nBefore starting a metagenomic project/experiment, a list of considerations an... |
null | null | null | dx.doi.org/10.17504/protocols.io.ek3bcyn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
For <a href="https://www.protocols.io/view/Transcriptomics-During-One-Step-Growth-Curves-for-dem3c5" target="_blank">Transcriptomics During One-Step Growth Curves for Cellulophaga Phages protocol</a>.
[STEPS]
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null | null | null | dx.doi.org/10.17504/protocols.io.nppddmn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Basic protocol to achieve lipofectamine transfection of Human Embryonic Kidney 293 (HEK293) cells with cDNA and/or siRNA.</p>
[BEFORE_START]
<p style="text-align: left;">Make complete DMEM:</p>
<p style="text-align: center;"> </p>
<table style="height: 105px;" width="312">
<... | [] |
80,202 | Mortality in patients with COVID-19 versus non-COVID-19- related acute respiratory distress syndrome: A single center retrospective observational cohort study | 1 | dx.doi.org/10.17504/protocols.io.bp2l6961rlqe/v2 | https://www.protocols.io/view/mortality-in-patients-with-covid-19-versus-non-cov-csjiwcke | Yu-Hsiang Hsieh, Han-Shui Hsu | TITLE: Mortality in patients with COVID-19 versus non-COVID-19- related acute respiratory distress syndrome: A single center retrospective observational cohort study
AUTHORS: Yu-Hsiang Hsieh, Han-Shui Hsu
[DESCRIPTION]
The pathophysiology of coronavirus disease-2019 (COVID-19)-related acute respiratory distress syndro... | ["Study population\nThis single center retrospective observational cohort study included patients with COVID-19 and non-COVID-19-related ARDS that required invasive mechanical ventilation. \n\nAll patients with COVID-19 had positive real-time polymerase chain reaction (RT-PCR) results for severe acute respiratory syndr... |
36,839 | Quick-Hot-Gram-Cromotropo QHGC lugol solution (Agudelo-Lopez SP and Montoya-Palacio MN, 2004) | 1 | dx.doi.org/10.17504/protocols.io.bf8fjrtn | https://www.protocols.io/view/quick-hot-gram-cromotropo-qhgc-lugol-solution-agud-bf8fjrtn | Javier Antonio Benavides | TITLE: Quick-Hot-Gram-Cromotropo QHGC lugol solution (Agudelo-Lopez SP and Montoya-Palacio MN, 2004)
AUTHORS: Javier Antonio Benavides
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Lugol's solution is an aqueous solution which contains iodine (I</span><span style = "vertical-align:sub;">2</s... | ["Homogenize the sample well with a wooden toothpick in the container that contains it", "Make a grade spread of approximately 2 cm long by 2 cm wide, sliding the stick impregnated with fecal matter onto a new degreased, dry, or used but clean and scratch-free slide.", "Remove excess stool with a clean, chopped wooden ... |
85,095 | Sanger Tree of Life Sample Homogenisation: Covaris cryoPREP® Automated Dry Pulverizer | 4 | dx.doi.org/10.17504/protocols.io.eq2lyjp5qlx9/v1 | https://www.protocols.io/view/sanger-tree-of-life-sample-homogenisation-covaris-cxcfxitn | Juan Pablo Narváez-Gómez, Haddijatou Mbye, graeme oatley, Michelle Strickland, Caroline Howard | TITLE: Sanger Tree of Life Sample Homogenisation: Covaris cryoPREP® Automated Dry Pulverizer
AUTHORS: Juan Pablo Narváez-Gómez, Haddijatou Mbye, graeme oatley, Michelle Strickland, Caroline Howard
[DESCRIPTION]
This protocol describes the procedure for cryogenic homogenisation of tissue samples using the Covaris cryo... | ["[Disruption] Power on the cryoPREP instrument. Ensure all doors to the room are closed and all room occupants are wearing ear defenders. Set the setting dial to “1”.", "[Transfer sample to TissueTUBE] Place the sample into the tissueTUBE TT1 and seal using the adapter and attaching the sample tube on the top.", "[Tra... |
65,064 | LDM protocol for estimating plasmid conjugation rates | 4 | null | https://www.protocols.io/view/ldm-protocol-for-estimating-plasmid-conjugation-ra-cbsgsnbw | Olivia Kosterlitz, Claire Wate | TITLE: LDM protocol for estimating plasmid conjugation rates
AUTHORS: Olivia Kosterlitz, Claire Wate
[DESCRIPTION]
This is a general protocol to implement the LDM approach for estimating plasmid conjugation rates. This version of the protocol was originally submitted with the accompanying manuscript. The recommende... | ["[Phase 1: Minimum inhibitory concentration assay with the transconjugant-selecting medium. medium.] Prepare bacterial cultures.\n\n Start cultures from freezer stocks of the donors, recipients, and transconjugants. Supplement the donor and transconjugant growth culture medium with the appropriate selection to maintai... |
67,635 | Fixation, Immunohistochemistry and in situ Hybridization of Human Lung Organoids | 1 | dx.doi.org/10.17504/protocols.io.e6nvwk5p2vmk/v3 | https://www.protocols.io/view/fixation-immunohistochemistry-and-in-situ-hybridiz-ceattaen | Morris Baumgardt, Maren Hülsemann,, Katharina Hellwig, Alina Langenhagen, Anne Voss, Simon Dökel, Achim D. Gruber, Stefan Hippenstiel, Andreas C. Hocke, Katja Hönzke | TITLE: Fixation, Immunohistochemistry and in situ Hybridization of Human Lung Organoids
AUTHORS: Morris Baumgardt, Maren Hülsemann,, Katharina Hellwig, Alina Langenhagen, Anne Voss, Simon Dökel, Achim D. Gruber, Stefan Hippenstiel, Andreas C. Hocke, Katja Hönzke
[DESCRIPTION]
This protocol describes the fixation of i... | ["[Fixation] Remove the organoid medium from the organoid containing well. Organoids should be collected from minimum two wells of a 24-well plate, to obtain a sufficient amount of organoids for staining.", "[Fixation] Add 1 mL cold base medium and collect Cultrex with organoids in a tube, flush well with 1 mL base med... |
94,450 | Characterization of human immune cell subpopulations in cerebrospinal fluid using mass cytometry. | 5 | dx.doi.org/10.17504/protocols.io.36wgqjp4ovk5/v2 | https://www.protocols.io/view/characterization-of-human-immune-cell-subpopulatio-c8gsztwe | Gerardina Gallaccio, Meng Wang, Stephan Schlickeiser, Desiree Kunkel, chotima.boettcher, Camila Fernández-Zapata | TITLE: Characterization of human immune cell subpopulations in cerebrospinal fluid using mass cytometry.
AUTHORS: Gerardina Gallaccio, Meng Wang, Stephan Schlickeiser, Desiree Kunkel, chotima.boettcher, Camila Fernández-Zapata
[DESCRIPTION]
Phenotypic and compositional changes of immune cells in cerebrospinal fluid (... | ["[Sample collection and storage] Prepare the anchor sample. \n\nAn anchor sample is peripheral blood mononuclear cells (PBMCs) used as internal reference across different measurements/batches to facilitate the signal normalization8.\nHowever, cell types other than PBMCs can also be used as an anchor sample but they sh... |
28,905 | Dural Cell Isolation | 1 | dx.doi.org/10.17504/protocols.io.8ghhtt6 | https://www.protocols.io/view/dural-cell-isolation-8ghhtt6 | Andrea Argouarch | TITLE: Dural Cell Isolation
AUTHORS: Andrea Argouarch
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Isolation of cells from human dura mater. Protocol includes tissue freezing, cutting the tissue with surgical tools, plating into a 6 well plate, placing a coverslip on top of the tissue, and addin... | ["[Preparation for Isolation]\nPrepare solid autoclaving a. 25 mm coverslips – 7 coverslips per 13 cm pouch (slide coverslips in the middle of the pouch before opening) b. Surgical Tools – 1 each per 23 cm pouch i. Dumont # 5 Forceps ii. Tungsten Scissors c. Seal autoclave pouch and autoclave. ... |
21,909 | Single Nucleus Drop-seq (snDrop-seq) | null | dx.doi.org/10.17504/protocols.io.zmvf466 | null | Song Chen, Blue B. Lake, Sarah Urata, Kun Zhang | TITLE: Single Nucleus Drop-seq (snDrop-seq)
AUTHORS: Song Chen, Blue B. Lake, Sarah Urata, Kun Zhang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The protocol presented here is a Drop-Seq protocol modified for single nuclei. </div><div class = "text-block">The original Drop-Seq protocol comes fro... | ["[Droplet Formation]\nPrepare Pump SystemPower on the syringe pumps (switches located on the back left of the pump)Set up correct flow rates using the screen on the pumpOil: 15,000 ul/hrCells: 4,000 ul/hrBeads: 4,000 ul/hr", "[Droplet Formation]\nPrepare microfluidic cellCut and remove protective plastic t... |
44,562 | Light Sheet Fluorescence Microscopy Image Acquisition | 1 | dx.doi.org/10.17504/protocols.io.bprsmm6e | https://www.protocols.io/view/light-sheet-fluorescence-microscopy-image-acquisit-bprsmm6e | Seth Currlin, Marda Jorgensen, Jerelyn Nick | TITLE: Light Sheet Fluorescence Microscopy Image Acquisition
AUTHORS: Seth Currlin, Marda Jorgensen, Jerelyn Nick
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The </span><a href="https://www.zeiss.com/microscopy/int/cmp/lsc/20/light-sheet-microscopy/new-zeiss-lightsheet-7.html?utm_medium=cp... | ["[Refractive Index (R.I.) Matching]\nRefractive index matching solution (RIMS)After tissue clearing, using procedures such as CLARITY, a final matching of refractive index of the tissue with imaging medium is required. Acquisition system settings and objectives determine what refractive index to adjust for. This three... |
29,423 | DNA extraction from water/soil: 50-50-50 buffer-chloroform/phenol method | null | dx.doi.org/10.17504/protocols.io.8yphxvn | null | Stef van der Merwe | TITLE: DNA extraction from water/soil: 50-50-50 buffer-chloroform/phenol method
AUTHORS: Stef van der Merwe
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is derived from the "DNA extraction from water: 50-50-50 buffer-chloroform/phenol method" designed by The Department of Envi... | ["[Sample preparation]\nMembrane filtersIn an aseptic environment, such as a laminar flow hood, use sterile forceps to place a membrane filter (containing concentrated bacteria) into a petri dish. With flame-sterilised scissors, cut the membrane filter into small pieces (~ 0.5 - 1 cm2). Place approximately 8-10 pieces ... |
51,931 | genomic DNA-extraction | 4 | dx.doi.org/10.17504/protocols.io.bwx3pfqn | https://www.protocols.io/view/genomic-dna-extraction-bwx3pfqn | Michael Burgis | TITLE: genomic DNA-extraction
AUTHORS: Michael Burgis
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">DNA isolation protocol for quick and rapid extraction of genomic DNA from Chlamydomonas reinhardtii cells. (also works for cyanobacteria)</div><div class = "text-block"><span>This protocol is bas... | ["[Buffer preparation]\nTEN Buffer (10 mM Tris-HCl, 10 mM EDTA, 150 mM NaCl)SDS-EB Buffer (2% SDS, 400 mM NaCl, 40 mM EDTA, 100 mM Tris-HCl, pH 8.0)TE Buffer (10mM Tris-HCl pH 8.0, 1mM EDTA pH 8.0) [autoclaved]", "[Resuspension and lysis]\nPellet the 10ml overnight culture of your algae or cyanobacteria in a 15ml falco... |
62,930 | Pain And Mood Assessment in Cancer Patients In A Tertiary Care Hospital | 1 | dx.doi.org/10.17504/protocols.io.261gen9dog47/v1 | https://www.protocols.io/view/pain-and-mood-assessment-in-cancer-patients-in-a-t-b9psr5ne | Pradyuman Singh Rajput, Dhruv Patel, Neel Modi, Aakash Jirafe, Dr Steffi John, PharmD | TITLE: Pain And Mood Assessment in Cancer Patients In A Tertiary Care Hospital
AUTHORS: Pradyuman Singh Rajput, Dhruv Patel, Neel Modi, Aakash Jirafe, Dr Steffi John, PharmD
[DESCRIPTION]
Cancer Patients often suffer from mixed aetiologies of pain referred to as cancer pain.
The study was conducted to assess various ... | ["[PRIOR REQUIREMENTS] Equipping Investigator with Pre-Requisite counselling with the patient.", "[PRIOR REQUIREMENTS] Investigator should know about the patient using Medication Records and attending nurse.", "[Data Collection] Collecting Demographics and Patient Vitals from Patient file.", "[Data Collection] Descript... |
81,401 | Microfluidic Chip Production v1.1 | 1 | dx.doi.org/10.17504/protocols.io.6qpvrdq7pgmk/v4 | https://www.protocols.io/view/microfluidic-chip-production-v1-1-ctqzwmx6 | Florian De Rop, Stein Aerts, Suresh Poovathingal | TITLE: Microfluidic Chip Production v1.1
AUTHORS: Florian De Rop, Stein Aerts, Suresh Poovathingal
[DESCRIPTION]
Protocol for producing microfluidic chips used in HyDrop experiment.
[STEPS]
SECTION: Microfluidic Chip Preparation
1. Producing an SU-8 patterned silicon wafer
Here, we describe how we produce our microfl... | ["[Microfluidic Chip Preparation] Producing an SU-8 patterned silicon wafer\nHere, we describe how we produce our microfluidic chips. The most important part is that the x/y dimensions of your droplet generators match ours. The z-dimension (channel height) may vary according to your method of spin-coating and the visco... |
null | null | null | dx.doi.org/10.17504/protocols.io.mf9c3r6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Recent attempts to replicate the ego depletion effect have often failed. The goal of this study is to shed light on research experiences and practices regarding ego depletion. A PubMed search resulted in 1721 researchers who had previously published on ego depletion. They wer... | [] |
54,455 | Validation of manual blood culture bottles | 1 | dx.doi.org/10.17504/protocols.io.bzexp3fn | https://www.protocols.io/view/validation-of-manual-blood-culture-bottles-bzexp3fn | Sien Ombelet, Liselotte Hardy, Jan Jacobs | TITLE: Validation of manual blood culture bottles
AUTHORS: Sien Ombelet, Liselotte Hardy, Jan Jacobs
[DESCRIPTION]
Use of equipment-free, “manual” blood cultures is still widespread in low-resource settings, as requirements for implementation of automated systems are often not met. Quality of manual blood culture ... | ["[Spiking of the blood (human or horse)] Spiking of the blood (human or horse) is done with frozen (-80°C) clinical or ATCC strains", "[Spiking of the blood (human or horse)] Strains to be tested are taken from the -80°C freezer (conservation on microbeads) and plated out on blood agar. The plates are incubated for 18... |
29,007 | DNA cloning | null | dx.doi.org/10.17504/protocols.io.8jphumn | null | Laura Sánchez | TITLE: DNA cloning
AUTHORS: Laura Sánchez
[STEPS] | [] |
32,984 | Seawater sample preparation for microplastic determination | null | dx.doi.org/10.17504/protocols.io.bcfyitpw | null | Mª Dolores Gelado Caballero, Tania Montoto Martínez | TITLE: Seawater sample preparation for microplastic determination
AUTHORS: Mª Dolores Gelado Caballero, Tania Montoto Martínez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The following protocol is fit for seawater sample preparation prior to its observation under a stereomicroscope for the deter... | ["Clean the glass beaker where your seawater sample is transfered: rinse it thoroughly three times withNote down the volume.", "Prepare the vacuum filtration system with a glass microfibre filter (0.7 μm; GF/F ø=47 mm) and filter the full volume.", "Rinse the vacuum filtration system three times while it continues fil... |
37,409 | Optogenetically stimulating enteric neurons in the murine large intestine. | null | dx.doi.org/10.17504/protocols.io.bgr9jv96 | https://www.protocols.io/view/optogenetically-stimulating-enteric-neurons-in-the-bgr9jv96 | Dante Heredia, Thomas Gould | TITLE: Optogenetically stimulating enteric neurons in the murine large intestine.
AUTHORS: Dante Heredia, Thomas Gould
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for optogenetically stimulating neuronal subtypes in murine colonic myenteric plexus. </div></div>
[STEPS]
?. Dissection an... | ["Dissection and experiments are done in the dark under infrared illumination. A ventral midline incision is made and the whole colon is carefully excised into a Sylguard lined dissection dish containing oxygenated Krebs-ringer solution.", "The colon is then drawn over a 1.5-mm diameter fire-polished capillary tube, w... |
null | null | null | dx.doi.org/10.17504/protocols.io.szvef66 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Textos utilizados para evaluar síntomas visuales y oculares asociados al uso de la lectura con smartphones. Hay cuatro textos descritivos sobre una especie animal (abejas, koalas, ornitorrincos y kanguros) junto con plantilla enla que se indican las palabras suprimidas utiliz... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.vj7e4rn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Purification of mammalian orthoreovirus by CsCl gradient
[BEFORE_START]
Reagents
HO Buffer
1 mL 1 M Tris, p 7.4
5 mL 5 M NaCl
67 uL B-ME
Water to 100 mL
Filter sterilize through 0.2 micron membrane
Dialysis Buffer
120 mL 5M NaCl
60 mL 1M MgCl2
40 mL 1M Tris, pH 7.4
water to... | ["{\"blocks\":[{\"key\":\"2hfrk\",\"text\":\"Pellet 4x108 spinner-adapted L929 at 2000 x g for at .\",\"type\":\"unstyled\",\"depth\":0,\"inlineStyleRanges\":[{\"offset\":11,\"length\":1,\"style\":\"sup\"}],\"entityRanges\":[{\"offset\":50,\"length\":1,\"key\":0},{\"offset\":55,\"length\":1,\"key\":1}],\"data\":[]},... |
null | null | null | dx.doi.org/10.17504/protocols.io.nkidcue | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>It is a crossover, double-blind, sham-controlled, pseudorandomized, and counterbalanced study at the Laboratory of Applied Neuroscience (LANA) of the Federal University of Pernambuco (UFPE). We performed a double-blind, randomized, sham-controlled crossover study with 12 heal... | [] |
28,301 | Demultiplexing Nanopore reads with LAST | null | dx.doi.org/10.17504/protocols.io.7vmhn46 | null | David Eccles | TITLE: Demultiplexing Nanopore reads with LAST
AUTHORS: David Eccles
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is for a semi-manual method for read demultiplexing, as used after my presentation </span><span style = "font-style:italic;">Sequencing DNA with Linux Cores and Na... | ["[Generating Barcode Index]\nPrepare a FASTA file containing barcode sequences (see attached FASTA file). To reduce the chance of mismatched adapters, this should only contain the barcode sequences. That restriction means this approach will not work for short reads, where the barcode sequences are very likely to occur... |
42,616 | OPAT in an area with a high prevalence of MDR bacteria | 1 | dx.doi.org/10.17504/protocols.io.bmuyk6xw | https://www.protocols.io/view/opat-in-an-area-with-a-high-prevalence-of-mdr-bact-bmuyk6xw | Thais Salles, Eduardo Alexandrino Medeiros | TITLE: OPAT in an area with a high prevalence of MDR bacteria
AUTHORS: Thais Salles, Eduardo Alexandrino Medeiros
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Objectives:</span><span> To identify factors associated with hospital admission and mortality within the... | ["This was a retrospective cohort study conducted between October 2016 and June 2017. The patients evaluated were among those treated by OPAT via the Santa Helena/Amil UnitedHealth Group network, which comprises the 137-bed Santa Helena Hospital, a tertiary care hospital located in the city of Santo André, in the Brazi... |
106,735 | ICA Data Ingestion Protocol | 0 | dx.doi.org/10.17504/protocols.io.n92ld8188v5b/v1 | https://www.protocols.io/view/ica-data-ingestion-protocol-dkgp4tvn | Gordon Qian, Ryan Davis, Jennifer Johnston | TITLE: ICA Data Ingestion Protocol
AUTHORS: Gordon Qian, Ryan Davis, Jennifer Johnston
[DESCRIPTION]
Step-by-step protocol for uploading genome sequencing data into the Neuronal Genome Atlas for Parkinsons (NGAP). This Atlas resource is hosted on Illumina Connected Analytics (ICA). The Ingestion Protocol
outlines main... | ["[Data ingestion methods] Data ingestion can be performed via different methods where one may be preferred over the other due to data storage location or the user’s operating system.", "[Data ingestion methods] Primary Upload method\n \nIllumina’s Command Line Interface (CLI) which can be executed locally or from... |
23,171 | UC Davis - Digestible Energy by Proximate Analysis | null | dx.doi.org/10.17504/protocols.io.2vbge2n | null | Trina Knotts | TITLE: UC Davis - Digestible Energy by Proximate Analysis
AUTHORS: Trina Knotts
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Changes in fecal energy loss can result in differences in net energy balance and feed effi... | ["Mice are singly housed in clean cages with fresh food and water and low bedding.", "Weigh mouse and “food-in” (grams of rodent diet provided at start of experiment).", "Save several pellets of rodent diet for analysis (e.g., for energy or macronutrient content)-Store at 4C in airtight container.", "At 24h, weigh mou... |
50,250 | RNA Extraction and RIN assessment. | 4 | null | https://www.protocols.io/view/rna-extraction-and-rin-assessment-bvbin2ke | Marcos Nascimento | TITLE: RNA Extraction and RIN assessment.
AUTHORS: Marcos Nascimento
[DESCRIPTION]
Adapted from Mauricio Rodriguez-Lanetty
[GUIDELINES]
Important:
Work in the fume hood in steps 1-7
Do not worry about RNases in steps 1-5. Your sample is full of them anyway. They are inhibited as long as they are in Trizol.
From st... | ["[RNA Extraction] Homogenize the starting material using a TissueRuptor and the appropriate volume of Trizol (see table, check Trizol instructions).", "[RNA Extraction] Optional: Centrifuge for 10 min at 12,000xg at 4C to eliminate debris and polysaccharides.12000 rcf, 10 min, 4 °C . Collect the supernatant.", "[RNA E... |
103,192 | Generating Ezrin Plasmids | 0 | dx.doi.org/10.17504/protocols.io.kqdg32361v25/v1 | https://www.protocols.io/view/generating-ezrin-plasmids-dgzy3x7w | Shiyi Wang | TITLE: Generating Ezrin Plasmids
AUTHORS: Shiyi Wang
[DESCRIPTION]
Generating Ezrin Plasmids
[STEPS]
1. 1. pZac2.1-GfaABC1D-BioID2-HA Construction
1.1. - **Obtain Materials**
1.2. - pZac2.1-GfaABC1D-Lck-GCaMP6f plasmid from Dr. Baljit Khakh (Addgene plasmid #52924).
1.3. - pAAV-hSyn-BioID2-Linker-Synapsin1a-HA plasmi... | ["1. pZac2.1-GfaABC1D-BioID2-HA Construction", "- **Obtain Materials**", "- pZac2.1-GfaABC1D-Lck-GCaMP6f plasmid from Dr. Baljit Khakh (Addgene plasmid #52924).", "- pAAV-hSyn-BioID2-Linker-Synapsin1a-HA plasmid for BioID2 sequence.", "- **PCR Amplification of BioID2**", "- PCR amplify BioID2 sequence from pAAV-hSyn-Bi... |
98,424 | Early Longitudinal Imaging in the Parkinson’s Progression Markers Initiative Using [ 18F] AV-133 (PPMI AV-133 Prodromal Imaging) | 0 | dx.doi.org/10.17504/protocols.io.bp2l62nqkgqe/v1 | https://www.protocols.io/view/early-longitudinal-imaging-in-the-parkinson-s-prog-dccy2sxw | Kenneth Marek | TITLE: Early Longitudinal Imaging in the Parkinson’s Progression Markers Initiative Using [ 18F] AV-133 (PPMI AV-133 Prodromal Imaging)
AUTHORS: Kenneth Marek
[DESCRIPTION]
This protocol details early longitudinal imaging in the Parkinson’s progression markers initiative using [ 18F] AV-133 (PPMI AV-133 Prodromal Imag... | ["[PURPOSE OF STUDY] The Parkinson Progression Marker Initiative (PPMI) is a longitudinal, observational, multi-center natural history study to assess progression of clinical features, digital outcomes, and imaging, biologic and genetic markers of Parkinson’s disease (PD) progression in study participants with manifest... |
46,496 | Labeled microtubules for single-molecule imaging | 4 | dx.doi.org/10.17504/protocols.io.bp2l6bdedgqe/v1 | https://www.protocols.io/view/labeled-microtubules-for-single-molecule-imaging-brm8m49w | John Salogiannis | TITLE: Labeled microtubules for single-molecule imaging
AUTHORS: John Salogiannis
[DESCRIPTION]
This protocol is for making labeled taxol-stabilized microtubles to be used for single-molecule imaging assays by adhering to biotin slides.
[BEFORE_START]
Please take notice of the buffer preparation in the Materials sec... | ["[Create taxol-stabilized labeled microtubules (can be reused for multiple weeks):] In a prechilled 1.5 mL Eppendorf tube, make a 10 µL mixture of 10 mg/mL. \nThe mixture should be 80% unlabeled, 10% biotin-tubulin, and 10% 405-tubulin. \nMix by gently flicking.", "[Create taxol-stabilized labeled microtubules (can be... |
36,752 | Creating Bacterial Glycerol Stocks for Long-term Storage | null | dx.doi.org/10.17504/protocols.io.bf5qjq5w | https://www.protocols.io/view/creating-bacterial-glycerol-stocks-for-long-term-s-bf5qjq5w | Priota Islam | TITLE: Creating Bacterial Glycerol Stocks for Long-term Storage
AUTHORS: Priota Islam
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Bacterial glycerol stocks are important for long-term storage. Bacteria on LB agar plate can be stored at 4°C for a few weeks. However, if you want to store bacteria ... | ["[Steps]\nFollow the protocol for Inoculating a Liquid Bacterial Culture", "[Steps]\nAfter you have bacterial growth, add 500 μL of the overnight culture to 500 μL of 50% glycerol in a 2 mL screw top tube or cryotube and gently mix", "[Steps]\nFreeze the glycerol stock tube at -80°C. The stock is now stable for years,... |
90,031 | ONT 16S Barcoding & Flow Cell Priming | 4 | dx.doi.org/10.17504/protocols.io.q26g7pd11gwz/v1 | https://www.protocols.io/view/ont-16s-barcoding-amp-flow-cell-priming-c36pyrdn | Emily Gailey | TITLE: ONT 16S Barcoding & Flow Cell Priming
AUTHORS: Emily Gailey
[DESCRIPTION]
This protocol describes how to carry out rapid barcoding of 16S amplicons using the 16S Barcoding Kit 1-24 (SQK-16S024). Due to the presence of both highly conserved (adequate for universal primers and phylogenetic signal) and highly ... | ["[Library Preparation with 16S Barcodes] Take one 96-well plate containing 16S barcodes. Break one set of barcodes (1-24, or as desired) away from the plate and return the rest to storage.\n\n*Important: The 96-well plates are designed to break in one direction only. Strips, or multiple strips, of eight wells/barcodes... |
null | null | null | dx.doi.org/10.17504/protocols.io.e2kbgcw | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<p>Use with all Ultra Streptavidin Detection Kits.</p>
<p> </p>
<p>All steps should be done in a humidity chamber such as 926301 (http://www.biolegend.com/humidity-chamber-plus-11211.html)</p>
<p> </p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?... | [] |
46,035 | Introgression | 5 | dx.doi.org/10.17504/protocols.io.bq7tmznn | https://www.protocols.io/view/introgression-bq7tmznn | Graham Etherington | TITLE: Introgression
AUTHORS: Graham Etherington
[DESCRIPTION]
The European polecat (Mustela putorius) is a mammalian predator which breeds across much of Europe east to central Asia. In Great Britain, following years of persecution the European polecat has recently undergone a population increase due to legal protect... | ["[HyDe analyses] Note: Due to a bug, HyDe can't handle sequences > 2.1Gb (the size of a 32-bit signed integer), so you'll need to use Sanger snp-sites to create a snp-only dataset.\nThe following uses the consensus sequences created in Step 2.4 at:\nhttps://www.protocols.io/edit/gatk-nuclear-variant-discovery-and-cons... |
60,663 | Human Pancreas Processing | 4 | dx.doi.org/10.17504/protocols.io.n2bvj6dnblk5/v1 | https://www.protocols.io/view/human-pancreas-processing-b7gxrjxn | Jing Chen, Edward J Butfiloski, Clayton E Mathews, Martha Campbell-Thompson | TITLE: Human Pancreas Processing
AUTHORS: Jing Chen, Edward J Butfiloski, Clayton E Mathews, Martha Campbell-Thompson
[DESCRIPTION]
The pancreas is a combined endocrine and exocrine organ and is uniquely positioned in the upper abdomen between the stomach (posterior and superior margins), duodenum (proximal or ... | ["[Pancreas processing] Unpack the shipping container and verify the organ container is at an ice-cold receiving temperature. Open the organ container in a BSL2 biosafety cabinet. Verify contents include pancreas with attached fat, duodenum, and spleen. Record any deviations for shipping using the", "[Pancreas processi... |
96,198 | GSEA | 0 | dx.doi.org/10.17504/protocols.io.rm7vzxwmxgx1/v1 | https://www.protocols.io/view/gsea-c97ez9je | Karina Jhingan | TITLE: GSEA
AUTHORS: Karina Jhingan
[DESCRIPTION]
This is a GSEA and GSVA analysis on time series data that creates barplots showing how the enrichment score varies over the series of time
[STEPS]
SECTION: Load Libraries
2. uncomment installs if needed
SECTION: Introduction
1. This pipeline is based off of http://... | ["[Load Libraries] uncomment installs if needed", "[Introduction] This pipeline is based off of http://yulab-smu.top/biomedical-knowledge-mining-book/universal-api.html", "[Load & Tidy Data] reading in log fold change data (this was a excel sheet saved as a csv where column 1 is gene names and column 2 is the log f... |
28,423 | PCR and cloning | null | dx.doi.org/10.17504/protocols.io.7zfhp3n | null | Norfitriah Mohamed Sohaimi, Mohd Hair Bejo, Abdul Rahman Omar, Aini Ideris, Nurulfiza Mat Isa | TITLE: PCR and cloning
AUTHORS: Norfitriah Mohamed Sohaimi, Mohd Hair Bejo, Abdul Rahman Omar, Aini Ideris, Nurulfiza Mat Isa
[STEPS] | [] |
89,380 | Isolation of microbes from the skin of terrestrial frogs | 4 | dx.doi.org/10.17504/protocols.io.kxygx35zzg8j/v1 | https://www.protocols.io/view/isolation-of-microbes-from-the-skin-of-terrestrial-c3icykaw | Stephanie N. Caty, Cooper Vasek, Marie-Therese Fischer, Amanda Muñoz Meneses, Daniel A. Shaykevich, Lauren A O'Connell | TITLE: Isolation of microbes from the skin of terrestrial frogs
AUTHORS: Stephanie N. Caty, Cooper Vasek, Marie-Therese Fischer, Amanda Muñoz Meneses, Daniel A. Shaykevich, Lauren A O'Connell
[DESCRIPTION]
The microbes on amphibian skin are critical for host health. Beneficial skin microbes regulate the growth of othe... | ["[Prepare plates for isolation of microbes] Prepare a number of rich, non-specific media plates for growing as many strains as possible. One or all types could be used, or alternative media could be used when appropriate. All media are autoclaved at 121 °C to sterility and specific times depend upon the volume of medi... |
46,935 | replication_files_Berger-et-al_COVID_GOOGLE | 3 | dx.doi.org/10.17504/protocols.io.br3xm8pn | https://www.protocols.io/view/replication-files-berger-et-al-covid-google-br3xm8pn | Lawrence M Berger, Giulia Ferrari, marion.leturcq , lidia.panico , Anne Solaz | TITLE: replication_files_Berger-et-al_COVID_GOOGLE
AUTHORS: Lawrence M Berger, Giulia Ferrari, marion.leturcq , lidia.panico , Anne Solaz
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Replication files for: </span><span style = "font-weight:bold;">COVID-19 Lockdowns and Demographically-Relev... | [] |
75,272 | Collections Standard Operating Protocol, Plant group: Vascular Plants | 1 | null | https://www.protocols.io/view/collections-standard-operating-protocol-plant-grou-cmrgu53w | Laura L Forrest, David Bell, Mruhsam, Michelle Hart | TITLE: Collections Standard Operating Protocol, Plant group: Vascular Plants
AUTHORS: Laura L Forrest, David Bell, Mruhsam, Michelle Hart
[DESCRIPTION]
This is part of the collection "DToL Taxon-specific Standard Operating Procedure (SOP) for the Plant Working Group". The SOP collection contains guidance on how to pro... | [] |
93,653 | Long Amplicon Nanopore Sequencing for Dual-Typing RdRp and VP1 Genes of Norovirus Genogroups I and II in Wastewater | 1 | dx.doi.org/10.17504/protocols.io.8epv5xpmjg1b/v1 | https://www.protocols.io/view/long-amplicon-nanopore-sequencing-for-dual-typing-c7pvzmn6 | George Scott, David Ryder, Mary Buckley, Richard Hill, Samantha Treagus, Tina Stapleton, David Walker, James Lowther, Frederico Batista | TITLE: Long Amplicon Nanopore Sequencing for Dual-Typing RdRp and VP1 Genes of Norovirus Genogroups I and II in Wastewater
AUTHORS: George Scott, David Ryder, Mary Buckley, Richard Hill, Samantha Treagus, Tina Stapleton, David Walker, James Lowther, Frederico Batista
[DESCRIPTION]
This protocol outlines the procedures... | ["[First-Round PCR]", "[PCR Product Quantification]", "[GI and GII PCR Product Pooling]", "[Native Barcoding and Sequencing] Perform end-prep and barcoding following the manufacturer’s instructions for ligation sequencing of amplicons in the Native Barcoding Kit 96 V14 by Oxford Nanopore Technologies", "[Native Barcodi... |
88,926 | Isolation of nuclei from mouse white adipose tissues for single-nucleus genomics --University of Minnesota TMCs | 1 | dx.doi.org/10.17504/protocols.io.rm7vzx56xgx1/v1 | https://www.protocols.io/view/isolation-of-nuclei-from-mouse-white-adipose-tissu-c236ygre | Ann Hertzel, Laura J Niedernhofer, David A Bernlohr | TITLE: Isolation of nuclei from mouse white adipose tissues for single-nucleus genomics --University of Minnesota TMCs
AUTHORS: Ann Hertzel, Laura J Niedernhofer, David A Bernlohr
[DESCRIPTION]
This protocol describes the steps to isolate and obtain total nuclei from frozen mouse white adipose tissues (WAT). We utiliz... | ["[Tissue Homogenization] Transfer 400 mg of gonadal adipose tissue (or 100 mg of inguinal adipose tissue) to a pre-cooled Petri dish on ice (Figure 1A).", "[Tissue Homogenization] Homogenize the tissue to release nuclei by applying 5 strokes with pestle A (loose) followed by 5\nstrokes with pestle B (tight) (Figures 1... |
62,614 | Green Ape CBD Gummies: Everything You Need to Know | 1 | dx.doi.org/10.17504/protocols.io.e6nvwko4wvmk/v1 | https://www.protocols.io/view/green-ape-cbd-gummies-everything-you-need-to-know-b9dwr27e | sildfgkivi | TITLE: Green Ape CBD Gummies: Everything You Need to Know
AUTHORS: sildfgkivi
[DESCRIPTION]
➢ Product Name — Green Ape CBD Gummies
➢ Category — Pain Relief
➢ Side-Effects — NA
➢ Main Benefits— Reduce anxiety, pain, and depression
➢ Hemp Quantity — 300mg per Bottle
➢ Health Warning — Keep Out of Reach of Children
➢ R... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.rmsd46e | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
51,859 | Gelatine bioplastic Ge01 | 1 | null | https://www.protocols.io/view/gelatine-bioplastic-ge01-bwvtpe6n | FabTextiles Clara Davis | TITLE: Gelatine bioplastic Ge01
AUTHORS: FabTextiles Clara Davis
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Gelatine bioplastic Ge01</span></div></div>
[STEPS]
?. Clean your surface and turn on hot plate.
?. Pour of cold water into your pot of gelatine .
2... | ["Clean your surface and turn on hot plate.", "Pour of cold water into your pot of gelatine .\n240 mL\n48 g", "Measure of Glycerol using a food scale and add it to the mixture. The amounts can be adjusted as long as the ratio remains roughly the same. Less Glycerol will result in a more brittle but harder material,... |
43,374 | How to make your protocol more reproducible, discoverable, and user-friendly | 1 | dx.doi.org/10.17504/protocols.io.bnknmcve | https://www.protocols.io/view/how-to-make-your-protocol-more-reproducible-discov-bnknmcve | Lenny Teytelman, protocols.io team, Anita Broellochs | TITLE: How to make your protocol more reproducible, discoverable, and user-friendly
AUTHORS: Lenny Teytelman, protocols.io team, Anita Broellochs
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">protocols.io offers extensive flexibility in entering and presenting detailed methods. However, simple sug... | ["[How to make your protocol easily discoverable]\nTitle: Try to make your title descriptive, as you would for a manuscript. This helps for searches on Google & protocols.io.", "[How to make your protocol easily discoverable]\nThumbnail Picture: Having a picture to identify the protocol helps you and other users find i... |
41,042 | ELISA for quantification of IL-11 in human serum. | 6 | dx.doi.org/10.17504/protocols.io.bkbsksne | https://www.protocols.io/view/elisa-for-quantification-of-il-11-in-human-serum-bkbsksne | Angel Justiz-Vaillant | TITLE: ELISA for quantification of IL-11 in human serum.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other body... | ["An anti-human IL-11 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-11 present in the serum sample binds to antibodies adsorbed into the microwells.", "The microplate is blocked with 3% non-fat milk-PBS buffer and... |
null | null | null | dx.doi.org/10.17504/protocols.io.nkjdcun | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<div title="Page 1">
<p><strong>Reagents to prepare for dissociation:</strong></p>
<div title="Page 1">
<ul>
<li>
<p>4 tissue dissociator tubes</p>
</li>
<li>
<p>4 falcon tube with 20ml Percoll solution 25% in PBS minus Ca<sup>+2</sup>Mg<sup>+2</sup> (cold)</p>
</li>
<li>
<p>4 fa... | [] |
34,892 | COVID-19 SCAN molecular workflow | null | dx.doi.org/10.17504/protocols.io.bebkjakw | null | Lea Starita | TITLE: COVID-19 SCAN molecular workflow
AUTHORS: Lea Starita
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify">Molecular Detection of SARS-CoV-2 for SCAN the Greater Seattle Coronavirus Assessment Network</div><style>
.justify:after {
... | ["Aliquot samples from the original upper respiratory sample found in Universal Transport Medium and transfer into barcoded matrix tubes (Thermo).", "Transfer of sample to the extraction plate and store the remainder of sample in .\n200 µl\n-80 °C", "Extract total nucleic acids using the Magna Pure 96 automated extrac... |
42,272 | BSCI:414 Lab 3 Analyze Agarose Gel Results and Create RNAse P Primers | 1 | null | https://www.protocols.io/view/bsci-414-lab-3-analyze-agarose-gel-results-and-cre-bmh8k39w | Harley King | TITLE: BSCI:414 Lab 3 Analyze Agarose Gel Results and Create RNAse P Primers
AUTHORS: Harley King
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">BSCI:414 Lab 3</div></div>
[STEPS]
?. [Review Lab 2 Experiment; Analyze Data]
Review Lab 2 hypothesis and experimental setup.
?. [Review Lab 2 Experi... | ["[Review Lab 2 Experiment; Analyze Data]\nReview Lab 2 hypothesis and experimental setup.", "[Review Lab 2 Experiment; Analyze Data]\nWatch experiment process video, pausing to discuss.https://youtu.be/SJoLg-GCeOY", "[Review Lab 2 Experiment; Analyze Data]\nAnalyze PCR fragment lengths on agarose gel. You can find a c... |
18,940 | Research on the application of mobile phone location signal data in earthquake emergency work | null | dx.doi.org/10.17504/protocols.io.wq4fdyw | null | xia chaoxu | TITLE: Research on the application of mobile phone location signal data in earthquake emergency work
AUTHORS: xia chaoxu
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">After the earthquake, the important task of the earthquake emergency rescue work is to minimize casualties, but due to the sudden e... | ["[the distribution of signal data]\nWe collected phone location data from jiuzhaigou county, the time period of data acquisition is from 2 hours before the earthquake to 8 hours after the earthquake(19:00 on August 8th and 5:00 on August 9th), total 10 hours of data. In contrast, we also collected data for the same pe... |
28,735 | Quantitative Magnetization Transfer MR Imaging (qMT-MRI) of Diabetic Mouse Kidney | null | dx.doi.org/10.17504/protocols.io.8a7hshn | null | Feng Wang, Takamune Takahashi | TITLE: Quantitative Magnetization Transfer MR Imaging (qMT-MRI) of Diabetic Mouse Kidney
AUTHORS: Feng Wang, Takamune Takahashi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">This protocol describes the procedures and... | ["MRI: All MR images were acquired on a 7T horizontal bore imaging system. A Doty 38-mm inner diameter transceiver coil was used due to the large size of the diabetic mice. Anesthesia was induced and maintained with a 1.5%/98.5% isoflurane/oxygen mixture, and a constant body temperature of 37.5ºC was maintained using h... |
20,127 | U Mass - Cytokines Panel III - multiplex | null | dx.doi.org/10.17504/protocols.io.xv7fn9n | null | Jason Kim | TITLE: U Mass - Cytokines Panel III - multiplex
AUTHORS: Jason Kim
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">
This experiment provides the quantification of multiple cytokines and chemokines using multiplexed-Lumi... | ["Decant Wash Buffer and remove the residual amount from all wells by inverting the plate and tapping it smartly onto absorbent towels several times.", "Add 25 μL of each Standard or Control solution into the appropriate wells. Assay Buffer should be used for 0 pg/mL standard (Background).", "Add 25 μL of Assay Buffer ... |
74,795 | Hestrin-Schramm (HS) medium | 4 | null | https://www.protocols.io/view/hestrin-schramm-hs-medium-cmaju2cn | Andreas Sagen | TITLE: Hestrin-Schramm (HS) medium
AUTHORS: Andreas Sagen
[DESCRIPTION]
Hestrin-Schramm medium is a common medium composition to grow Komagataeibacter. The medium contains glucose as a source for energy and carbon, while yeast extract and peptone are the primary nitrogen sources. Both sodium phosphate and magnesium ... | ["[100 mL Dextrose solution] All compounds are measured using a high precision analytical scale from powdered compounds. Each compound is measured to within 1% of the target weight. All compounds are mixed in a Duran bottle", "[100 mL Dextrose solution] Fill the bottle with 60 mL double-distilled water", "[100 mL Dextr... |
68,879 | In vitro GTPase activity | 1 | dx.doi.org/10.17504/protocols.io.q26g74qwqgwz/v1 | https://www.protocols.io/view/in-vitro-gtpase-activity-cfhptj5n | Xinbo Wang, Pietro De Camilli | TITLE: In vitro GTPase activity
AUTHORS: Xinbo Wang, Pietro De Camilli
[DESCRIPTION]
This protocol details methods for the in vitro GTPase activity testing of purified LRRK2.
[STEPS]
SECTION: In vitro GTPase activity
1. Set up the reaction mixtures in a 96-well plate with 5 µL 20× reaction buffer (1 Molarity (M) Tris... | ["[In vitro GTPase activity] Set up the reaction mixtures in a 96-well plate with 5 µL 20× reaction buffer (1 Molarity (M) Tris-HCl, 20 millimolar (mM) MgCl2, pH 7.5 and 2 millimolar (mM) sodium azide), 200 micromolar (µM) 2-amino-6-mercapto-7-methylpurine riboside, 0.1 U purine nucleoside phosphorylase, and 9 micromol... |
81,819 | NCEM Drop - Inactivation of sample on grid (TM-014) | 4 | dx.doi.org/10.17504/protocols.io.8epv59mr6g1b/v1 | https://www.protocols.io/view/ncem-drop-inactivation-of-sample-on-grid-tm-014-ct53wq8n | sandra.crameri | TITLE: NCEM Drop - Inactivation of sample on grid (TM-014)
AUTHORS: sandra.crameri
[DESCRIPTION]
NCEM Drop - inactivation of samples on grid
[GUIDELINES]
This procedure is used for inactivation of 3Z agents, useful if the virus has low titire.
[STEPS]
1. Adsorb 10 µL sample to grid 10 min
2. Immerse grid in drop o... | ["Adsorb 10 µL sample to grid 10 min", "Immerse grid in drop of 2.5 % volume in 0.1 Molarity (M) Sorenson's phosphate buffer 10 min", "Wash 0.1 Molarity (M) Sorenson's phosphate buffer", "Using filter paper wick excess buffer from grid - do not dry out, leave grid surface wet.", "Stain 1 min", "Using filter paper g... |
86,694 | Can light be used to treat obesity and diabetes? | 4 | dx.doi.org/10.17504/protocols.io.x54v9ppkpg3e/v1 | https://www.protocols.io/view/can-light-be-used-to-treat-obesity-and-diabetes-cywexxbe | Rédoane Daoudi | TITLE: Can light be used to treat obesity and diabetes?
AUTHORS: Rédoane Daoudi
[DESCRIPTION]
This document is highly theoretical lab method paper. It may be used to perform
thermogenesis from several cells in a living organism instead of only brown
adipocytes. We perform thermogenesis from white adipocytes. The pur... | ["[In vitro assays] Use a cell line: white adipose cells in DMEM medium.", "[In vitro assays] Transfect cells by electroporation and with the following DNA constructs:\n\n\n1) the light-driven\ninward H+ pump PoXeR targeted to the inner mitochondrial membrane: \n\n\n2) firefly luciferase \n\n\n3) luciferin-regenerating... |
28,586 | E. coli Colony PCR | null | dx.doi.org/10.17504/protocols.io.76ihrce | null | iGEM Dusseldorf | TITLE: E. coli Colony PCR
AUTHORS: iGEM Dusseldorf
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Ideally use at least two master mixes:</div><div class = "text-block">2 vector-specific primers (to determine insert size): </div><div class = "text-block">1 vector-specific + 1 gene-specific primer </... | [] |
42,534 | Latent class analyses on attendance of toddler safety promotion intervention | 1 | dx.doi.org/10.17504/protocols.io.bmsek6be | https://www.protocols.io/view/latent-class-analyses-on-attendance-of-toddler-saf-bmsek6be | George Washington University | TITLE: Latent class analyses on attendance of toddler safety promotion intervention
AUTHORS: George Washington University
[DESCRIPTION]
Objective: Little is known about the association between maternal depressive symptoms and attendance at safety promotion interventions. This study used latent class analysis (LCA) to ... | ["Inclusion criteria\nA subsample of those who were assigned to safety promotion interventiong group (n=91) out of the sample of all the mother-toddler dyads who participated in the a randomized toddler safety promotion intervention trial (n=277). For the mother-toddler dyads who particiated in the intervention trial, ... |
77,156 | General protocol for the culture of adherent mammalian cell lines | 1 | null | https://www.protocols.io/view/general-protocol-for-the-culture-of-adherent-mamma-cpkcvksw | Clark Fritsch | TITLE: General protocol for the culture of adherent mammalian cell lines
AUTHORS: Clark Fritsch
[DESCRIPTION]
The purpose of this protocol is to give a general overview of the various methods associated with the culture of adherent mammalian cells. These methods include the use of aseptic technique, maintaining mammal... | ["[Maintenance of Aseptic Technique and Setup of Work Environment] Mammalian cell lines are extremely vulnerable to bacterial and fungal contamination from the environment, as they do not have immune systems of their own. Because of this, extra care must be taken to avoid contamination. This section will cover the vari... |
46,564 | Left Ventricle Function | 5 | dx.doi.org/10.17504/protocols.io.brqcm5sw | https://www.protocols.io/view/left-ventricle-function-brqcm5sw | Giorgio Bozzi | TITLE: Left Ventricle Function
AUTHORS: Giorgio Bozzi
[STEPS]
?. | [] |
106,618 | Seahorse XF Cell Mito Stress Test | 0 | dx.doi.org/10.17504/protocols.io.36wgqn15ogk5/v1 | https://www.protocols.io/view/seahorse-xf-cell-mito-stress-test-dkc24sye | Isabel Lam, Alain Ndayisaba, Vikram Khurana | TITLE: Seahorse XF Cell Mito Stress Test
AUTHORS: Isabel Lam, Alain Ndayisaba, Vikram Khurana
[DESCRIPTION]
Seahorse XF Cell Mito Stress Test
[STEPS] | [] |
101,330 | Mouse handling to reduce stress and reactivity | 0 | dx.doi.org/10.17504/protocols.io.261ge55yog47/v1 | https://www.protocols.io/view/mouse-handling-to-reduce-stress-and-reactivity-de7s3hne | Michael Marcotte, Ashley Bernado, Nathaniel Linga, Carmina A. Pérez-Romero, Srija Das, Jean-Louis Guillou, Etienne Sibille, Thomas Prevot | TITLE: Mouse handling to reduce stress and reactivity
AUTHORS: Michael Marcotte, Ashley Bernado, Nathaniel Linga, Carmina A. Pérez-Romero, Srija Das, Jean-Louis Guillou, Etienne Sibille, Thomas Prevot
[DESCRIPTION]
This protocol provides a description of a mouse-handling technique which intends to minimize the stress... | ["[DAY 1: 5 minutes per mice] Gently open the cage and place the lid on the side, remove nesting materials, and other enrichment such as running wheels or shelters.", "[DAY 1: 5 minutes per mice] Introduce a gloved open hand to the home cage, slowly placing the hand along one side of the cage wall. \nDo not immediately... |
43,718 | Standard CD Measurements | 1 | dx.doi.org/10.17504/protocols.io.bnxemfje | https://www.protocols.io/view/standard-cd-measurements-bnxemfje | Rohanah Hussain, Charlotte S. Hughes, Giuliano Siligardi | TITLE: Standard CD Measurements
AUTHORS: Rohanah Hussain, Charlotte S. Hughes, Giuliano Siligardi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">CD spectroscopy is the essential tool to quickly ascertain in the far-UV region the global conformational changes, the secondary structure content, and ... | ["See 'Guidelines' section."] |
98,535 | Functional Characterization of the Human Islet Microvasculature Using Living Pancreas Slices | 4 | dx.doi.org/10.17504/protocols.io.kqdg36n27g25/v3 | https://www.protocols.io/view/functional-characterization-of-the-human-islet-mic-dcgf2ttn | Luciana Mateus Gonçalves, Joana Almaça | TITLE: Functional Characterization of the Human Islet Microvasculature Using Living Pancreas Slices
AUTHORS: Luciana Mateus Gonçalves, Joana Almaça
[DESCRIPTION]
Pancreatic islets are clusters of endocrine cells that secrete different hormones to regulate blood glucose levels. Efficient hormone secretion requires a cl... | ["[Methods] Human Organ Donors\n\nWe obtained human living pancreas slices from de-identified cadaveric donors (from the head of the pancreas, n = 6 non-diabetic individuals, male and female, ages from 20 – 59 years old; information on the donors used in this study is provided in Table S1) from the Network of Pancreati... |
22,939 | Carbon and nitrogen stable isotope analysis in harbor seal pup fur at CICESE | null | dx.doi.org/10.17504/protocols.io.2m3gc8n | null | Juan Carlos Herguera-García, Gisela Heckel | TITLE: Carbon and nitrogen stable isotope analysis in harbor seal pup fur at CICESE
AUTHORS: Juan Carlos Herguera-García, Gisela Heckel
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>In the Stable Isotope Laboratory at CICESE (Ensenada Center for Scientific Research and Graduate Education, Me... | [] |
80,186 | IMS Data Processing | 1 | dx.doi.org/10.17504/protocols.io.e6nvwjyj9lmk/v1 | https://www.protocols.io/view/ims-data-processing-csi2wcge | Lukasz Migas, Angela R.S. Kruse, Jamie Allen, ellie.l.pingry, Melissa Farrow, Jeff Spraggins, Raf Van De Plas | TITLE: IMS Data Processing
AUTHORS: Lukasz Migas, Angela R.S. Kruse, Jamie Allen, ellie.l.pingry, Melissa Farrow, Jeff Spraggins, Raf Van De Plas
[DESCRIPTION]
This protocol describes spectral alignment and mass calibration of IMS data beginning with Bruker (.d) raw files. Mass calibration is performed based on sever... | ["Extract the content of the Bruker (.d) raw file in pseudo-profile mode and at native spectral resolution into memory or into a format you can calculate within your compute environment of choice. If multiple regions of interest were acquired in the same experiment/file, split these into separate datasets to simplify s... |
88,829 | RSV Nested Amplicon Prep (from VarSkip Workflow) | 4 | null | https://www.protocols.io/view/rsv-nested-amplicon-prep-from-varskip-workflow-c2y5yfy6 | Parker Montfort | TITLE: RSV Nested Amplicon Prep (from VarSkip Workflow)
AUTHORS: Parker Montfort
[DESCRIPTION]
Use this modified protocol to prepare RSV Tiled amplicons for sequencing using the VarSkip Reagents and Workflow, with cleanup steps.This original protocol details methods for the NEBNext® ARTIC SARS-CoV-2 FS Library Prep Ki... | ["[cDNA Synthesis] Gently mix and spin down the LunaScript RT SuperMix reagent. Prepare the cDNA synthesis reaction as described below:", "[cDNA Synthesis] Incubate reactions in a thermocycler* with the following steps:", "[cDNA Amplification] Gently mix and spin down reagents. Prepare the split pool cDNA amplification... |
52,227 | extraccion de ARN en TRIzol | 4 | null | https://www.protocols.io/view/extraccion-de-arn-en-trizol-bw9bph2n | Marco Cacciabue, María Ines Gismondi | TITLE: extraccion de ARN en TRIzol
AUTHORS: Marco Cacciabue, María Ines Gismondi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocolo para extraccion de ARN a partir de TRIzol para virus de la fiebre aftosa</div></div>
[STEPS]
?. [Preparación]
Controlar cada uno de los siguiente puntos (cada... | ["[Preparación]\nControlar cada uno de los siguiente puntos (cada volumen es para 1 muestra a procesar)", "[Preparación]\nEnfriar la centrifuga refrigerada.", "[Preparación]\nLimpiar mesada de trabajo.", "[Preparación]\n200 μL de cloroformo.", "[Preparación]\n1 μL de glucógeno.", "[Preparación]\n700 μL de isopropanol."... |
92,560 | Stock solutions of cocaine, isradipine, nomifensine, lidocaine, DHβE, CP8, L-741,626, and water-soluble cholesterol | 1 | dx.doi.org/10.17504/protocols.io.yxmvm3bbbl3p/v1 | https://www.protocols.io/view/stock-solutions-of-cocaine-isradipine-nomifensine-c6mqzc5w | Katherine Brimblecombe, Stephanie J Cragg | TITLE: Stock solutions of cocaine, isradipine, nomifensine, lidocaine, DHβE, CP8, L-741,626, and water-soluble cholesterol
AUTHORS: Katherine Brimblecombe, Stephanie J Cragg
[DESCRIPTION]
This protocol details the making of the following stock solutions used in Brimblecombe, K.R. et al. (2023):cocaine (inhibits the ac... | ["[Cocaine (5 µM)] Make 50 mL aliquots of 10 mM stock solution:\nadd 3.4 mg per 1 mL dH2O\nstore at -20°C", "[Isradipine (5 µM)] Make 50 µL aliquots of 10 mM stock solution:\nadd 2.69 mL DMSO to 10 mg powder\nstored at -20°C", "[Cocaine (5 µM)] For each experiment, dilute 50 µL of 10 mM stock solution (one aliquot) in ... |
41,135 | ELISA for quantification of IL-15 in human serum. | 6 | dx.doi.org/10.17504/protocols.io.bkepktdn | https://www.protocols.io/view/elisa-for-quantification-of-il-15-in-human-serum-bkepktdn | Angel Justiz-Vaillant | TITLE: ELISA for quantification of IL-15 in human serum.
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other body cells. T... | ["An anti-human IL-15 coating antibody is adsorbed onto microwells by incubation overnight at 4°C.", "Add 50 µl of human serum. Human IL-15 present in the serum sample binds to antibodies adsorbed to the microwells.", "The microplate is blocked with 3% non-fat milk-PBS buffer and later wash to remove unbound proteins."... |
null | null | null | dx.doi.org/10.17504/protocols.io.hh6b39e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>In this protocol we publish the maps and sequences of specific plasmids designed for the transformation of Bigelowiella natans, Pyramimonas parkeae, Eutreptiella gymnastica, Chromera velia and Pseudonitzchia delicatissima. All these plasmids contain gene for firefly luciphera... | [] |
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