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 |
|---|---|---|---|---|---|---|---|
88,723 | Ex vivo mouse brain patch clamp recordings and Fura-2 imaging | 4 | dx.doi.org/10.17504/protocols.io.eq2lyj8zrlx9/v1 | https://www.protocols.io/view/ex-vivo-mouse-brain-patch-clamp-recordings-and-fur-c2vtye6n | taylor.panczyk | TITLE: Ex vivo mouse brain patch clamp recordings and Fura-2 imaging
AUTHORS: taylor.panczyk
[DESCRIPTION]
In this protocol we detail the steps to perform ex-vivo brain slices electrophysiology and Fura-2 recordings. For both types of recordings, the brain slices with the desired nucleus must be placed into the record... | ["[Prepare patch pipettes] Turn on the Sutter P-1000 puller and enter the desired pull protocol.", "[Prepare patch pipettes] Insert a thick-walled borosilicate glass capillary and press pull.", "[Prepare patch pipettes] Pipette resistance must be of 2.5 to 5 megaohms.", "[Setting up patch rig and environment] Turn on t... |
9,182 | Predicting_MWM_with_ANN | null | dx.doi.org/10.17504/protocols.io.k76czre | null | Akinori Higaki, Masaki Mogi, Jun Iwanami, Li-Juan Min, Hui-Yu Bai, Bao-Shuai Shan, Masayoshi Kukida, Harumi Kan-no, Shuntaro Ikeda, Jitsuo Higaki, Masatsugu Horiuchi | TITLE: Predicting_MWM_with_ANN
AUTHORS: Akinori Higaki, Masaki Mogi, Jun Iwanami, Li-Juan Min, Hui-Yu Bai, Bao-Shuai Shan, Masayoshi Kukida, Harumi Kan-no, Shuntaro Ikeda, Jitsuo Higaki, Masatsugu Horiuchi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">>> We would share the raw data and python scri... | ["[Raw_Data]"] |
94,861 | Production of α-synuclein preformed fibrils (PFF) | 4 | null | https://www.protocols.io/view/production-of-synuclein-preformed-fibrils-pff-c8vmzw46 | Tae-In Kam, Rong Chen, Valina L. Dawson, Ted Dawson | TITLE: Production of α-synuclein preformed fibrils (PFF)
AUTHORS: Tae-In Kam, Rong Chen, Valina L. Dawson, Ted Dawson
[DESCRIPTION]
This protocol outlines the procedure to produce preformed fibrils (PFF).
It has been adapted from Volpicelli-Daley et al., 2014
[STEPS]
SECTION: Generation of α-synuclein monomer
1. Tran... | ["[Generation of α-synuclein monomer] Transform α-synuclein plasmids (full length human α-synuclein cloned into pRK172 vector) into ClearColiTM BL21-competent E. coli, that have been genetically modified so that LPS does not trigger LPS-mediated immune response. From the small scale culture in LB medium, make a bacteri... |
38,266 | Protein Expression Using BL21(DE3), Large Scale (C2527) | 1 | dx.doi.org/10.17504/protocols.io.bhk2j4ye | https://www.protocols.io/view/protein-expression-using-bl21-de3-large-scale-c252-bhk2j4ye | New England Biolabs | TITLE: Protein Expression Using BL21(DE3), Large Scale (C2527)
AUTHORS: New England Biolabs
[DESCRIPTION]
This is the protocol for a large-scale Protein Expression Using BL21(DE3) Competent E. coli cells (C2527).
[BEFORE_START]
Determine the optimal time/temperature for the protein expression in a small scale tria... | ["Transform expression plasmid into BL21(DE3).", "Plate on antibiotic selection plates.", "Incubate at 37 °C.", "Inoculate 1 L with a freshly grown colony or with 10 mL.", "Incubate at 37 °C until OD600 reaches 0.4–0.8.", "Induce with 4 µL or 40 µL of 100 Milimolar (mM) (final concentration of 40 Micromolar (µM) or 4... |
54,431 | Glucosylceramidase Beta (GBA) Genotyping | 1 | dx.doi.org/10.17504/protocols.io.bzd7p29n | https://www.protocols.io/view/glucosylceramidase-beta-gba-genotyping-bzd7p29n | Huw Morris, Nigel Williams | TITLE: Glucosylceramidase Beta (GBA) Genotyping
AUTHORS: Huw Morris, Nigel Williams
[DESCRIPTION]
This protocol details the steps for GBA genotyping. This protocol has been adapted from the PRoBaND Clinical Consortium (incorporating methods described by Neuman et al., 2009 and Stone et al., 2000) and has been used fo... | ["[Primer Sequences] Use the following primer sequences:", "[Amplification of the GBA gene] Three different PCR reactions are performed. Refer to Table 2 for a detailed description of the PCR conditions used for each fragment.", "[Amplification of the GBA gene] In order to avoid amplification of the pseudogene, primer ... |
68,267 | Image Visualization and Proteoform Assignment of MALDI-MSI from LCMS Experimental Databases | 5 | null | https://www.protocols.io/view/image-visualization-and-proteoform-assignment-of-m-cewjtfcn | David J Degnan, Kevin J. Zemaitis, Dusan Velickovic, Mowei Zhou, Ljiljana.PasaTolic | TITLE: Image Visualization and Proteoform Assignment of MALDI-MSI from LCMS Experimental Databases
AUTHORS: David J Degnan, Kevin J. Zemaitis, Dusan Velickovic, Mowei Zhou, Ljiljana.PasaTolic
[DESCRIPTION]
Scope:
The protocol describes a workflow for processing mass spectrometry imaging (MSI) data of high resolution ... | ["[Data pre-processing] The .xml file from the MALDI source registering pixel coordinates is renamed to that of the .RAW file generated from the instrument, both files are then transferred to a separate imaging workstation after being backed up to an internal database.", "[Proteoform image visualization] Proteoforms ar... |
null | null | null | dx.doi.org/10.17504/protocols.io.nr3dd8n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A protocol for routine flash freezing of fruit fly samples prior to use in downstream protocols (e.g. RNA extraction).</p>
<p> </p>
<p> </p>
[BEFORE_START]
<p>Make sure you have the following items: LN<sub>2</sub>, dewar (~2L), a large rectangular Styrofoam tub, colored tim... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.dpu5nv | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Clearing zones on lawns of host bacteria potentially contain all lytic phages against the given host that were present in the original water sample. Little is still known about the occurrence and diversity of phages infecting specific hosts, but generally isolation procedures as... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.h93b98n | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Please contact Dr. Steven Wilhelm (wilhelm@utk.edu) for additional information regarding this protocol.</p>
<p> </p>
<p>Adapted from the original publication Morel, F. M. M., J. C. Westall, J. G. Reuter & J. P. Chaplick, 1975. Description of the algal growth media ‘Aquil’... | [] |
70,725 | Estimating microbial population data from optical density | 4 | dx.doi.org/10.17504/protocols.io.8epv5j6wjl1b/v1 | https://www.protocols.io/view/estimating-microbial-population-data-from-optical-chbdt2i6 | Portia M Mira, Pamela Yeh, Barry G. Hall | TITLE: Estimating microbial population data from optical density
AUTHORS: Portia M Mira, Pamela Yeh, Barry G. Hall
[DESCRIPTION]
The spectrophotometer has been used for decades to measure the density of bacterial populations as the turbidity expressed as optical density – OD. However, the OD alone is an unreliable me... | ["Preparation\n\nWhen calibrating a microtiter plate reader for microbial growth experiments, it is essential to begin with\na culture in which almost all the particles (cells) can form colonies, i.e., are colony-forming units or\nCFU. To achieve that, a mid-log phase culture is required - one in which the culture has ... |
45,035 | GenSwab Assay (SARS-CoV-2) | 4 | dx.doi.org/10.17504/protocols.io.bp8jmrun | https://www.protocols.io/view/genswab-assay-sars-cov-2-bp8jmrun | huiyi.chen , Sid Roy | TITLE: GenSwab Assay (SARS-CoV-2)
AUTHORS: huiyi.chen , Sid Roy
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The GenapSys SARS-CoV-2 GenSwab Assay is a reverse transcription sequencing (RT-Seq) test. The assay uses primers and probes that were first designed by OctantBio to detect RNA from SARS-... | ["[Pre-PCR: S2 Spike-in Dilution]\nStart with a stock solution of 1% Tween-20 in TE. Dilute 10x in TE to obtain 0.1% Tween-20 in TE.", "[Pre-PCR: S2 Spike-in Dilution]\nRetrieve S2 spike-in RNA from -80C freezer. S2 spike-in RNA is provided at 1e10 copies/ul. Perform three 100x dilutions, followed by a 10x dilution to ... |
73,946 | Harvesting and stocking cheese rind community samples | 4 | dx.doi.org/10.17504/protocols.io.x54v9dr7mg3e/v1 | https://www.protocols.io/view/harvesting-and-stocking-cheese-rind-community-samp-ckf2utqe | Emily C.P. Weiss | TITLE: Harvesting and stocking cheese rind community samples
AUTHORS: Emily C.P. Weiss
[DESCRIPTION]
This protocol describes how to harvest and stock cheese rind microbial community samples for a variety of purposes, including spatial imaging, metagenomics, metatranscriptomics, microbial isolation/culturing, and bacte... | ["[Rind scraping] Holding the cheese in one (gloved) hand and a sterile razor blade in the other, gently scrape the surface of the cheese to remove the rind biofilm. Avoid applying too much pressure, as you will start to dig into the paste. Scrape the rind biofilm into a weigh boat or other container to clean off the b... |
47,110 | Neural differentiation of AAVS1-TRE3G-NGN2 pluripotent stem cells | 1 | dx.doi.org/10.17504/protocols.io.br9em93e | https://www.protocols.io/view/neural-differentiation-of-aavs1-tre3g-ngn2-pluripo-br9em93e | Jiuchun Zhang, Harper JW | TITLE: Neural differentiation of AAVS1-TRE3G-NGN2 pluripotent stem cells
AUTHORS: Jiuchun Zhang, Harper JW
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is about neural differentiation of AAVS1-TRE3G-NGN2 pluripotent stem cells.</div></div>
[STEPS]
?. [Day 0:]
Treat H9 AAVS1-TRE3G-N... | ["[Day 0:]\nTreat H9 AAVS1-TRE3G-NGN2 cells with Accutase and plate the dissociated cells in matrigel-coated 6-well plates (2x105 cells/well) in ND1 Medium supplemented with Y27632 ().", "[Day 1:]\nReplace the medium with ND1 Medium.", "[Day 2:]\nReplace the medium with ND2 Medium.", "[Day 4:]\nExchange 50% of the medi... |
93,906 | SARS-CoV-2 Receptor Binding Domain Deoxy Fragment Sequencing | 4 | dx.doi.org/10.17504/protocols.io.261gedbp7v47/v1 | https://www.protocols.io/view/sars-cov-2-receptor-binding-domain-deoxy-fragment-c7xszpne | Noor Saber Jawad, Nuha Joseph Kandala | TITLE: SARS-CoV-2 Receptor Binding Domain Deoxy Fragment Sequencing
AUTHORS: Noor Saber Jawad, Nuha Joseph Kandala
[DESCRIPTION]
Since first reporting of SARS-CoV-2 case in China, there were urgent need to report and monitor emerging variants and keep track circulating mutation, in this methodology, we used simple, c... | ["[RNA Extraction] The RNA of SARS-CoV-2 extracted using Automated Extraction System ExiPrep‱ 96 Lite from Bioneer (South Korea) using the Exiprep 96 Viral DNA/RNA kit using the standard recommended procedure by the manufacturer.", "[cDNA synthesis] The extracted RNA used as a template to construct complementary DNA, c... |
26,555 | U Michigan - Intra-Epidermal Fiber Density | null | dx.doi.org/10.17504/protocols.io.563g9gn | null | Eva L. Feldman | TITLE: U Michigan - Intra-Epidermal Fiber Density
AUTHORS: Eva L. Feldman
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span><span style = "font-weight:bold;"> </span></div><div class = "text-block">Intra-epidermal nerve fiber density (IENFD) is used as ... | ["Reagents: Phosphate buffer (PB, 0.1 M, pH 7.2) SucroseEquipment: Razor blades, embedding molds, 24 well plateSolutions: 2% zamboni’s in phosphate buffer (PB, 0.1 M, pH 7.4) 30% sucrose in PBSProcedure:Fresh mouse or rat:\n1. Remove footpad and fix (4 hours) in 2% zamboni’s fixative for 4-6 hours.\n... |
74,326 | Co-extraction of RNA and DNA from soil and sediment samples | 1 | dx.doi.org/10.17504/protocols.io.rm7vzb6m4vx1/v1 | https://www.protocols.io/view/co-extraction-of-rna-and-dna-from-soil-and-sedimen-cktwuwpe | Dominik Buchner | TITLE: Co-extraction of RNA and DNA from soil and sediment samples
AUTHORS: Dominik Buchner
[DESCRIPTION]
This protocol describes extracting RNA and DNA from soil and sediment samples. 2 g of soil or up to 5 g of sediment can be processed in one extraction. The protocol is based on the RNeasy PowerSoil Total RNA Kit b... | ["[Cell lysis] Prepare one 15 mL conical centrifuge tube per sample by adding 0.5 g of a) 0.1 mm glass beads, b) 0.5 mm glass beads, c) 1 mm zirconia/silica beads d) 2 mm zirconia beads.", "[Cell lysis] Add up to 2 g of soil or up to 5 g of the sediment sample.", "[Cell lysis] Add 2.5 mL , 0.25 mL , 0.8 mL and 3.5 mL ... |
37,788 | RNA Synthesis with Modified Nucleotides (E2050) | 1 | dx.doi.org/10.17504/protocols.io.bg54jy8w | https://www.protocols.io/view/rna-synthesis-with-modified-nucleotides-e2050-bg54jy8w | New England Biolabs | TITLE: RNA Synthesis with Modified Nucleotides (E2050)
AUTHORS: New England Biolabs
[DESCRIPTION]
This is the synthesis protocol for modified nucleotides using the HiScribe™ T7 Quick High Yield RNA Synthesis Kit (E2050). The kit is capable of synthesizing biotin- or dye-modified RNA.
[BEFORE_START]
We strongly rec... | ["Thaw the necessary kit components.", "Mix and pulse-spin in microfuge to collect solutions to the bottoms of tubes.", "Assemble the reaction at Room temperature in the following order (Total reaction volume is 20 µL):", "Mix thoroughly and pulse-spin.", "Incubate at 37 °C for 120 min.", "Optional step: To remove temp... |
83,886 | Surgical procedures for simultaneous optogenetic manipulation in the SNc and acute fiber photometry in the dorsal striatum | 4 | dx.doi.org/10.17504/protocols.io.e6nvwd6qdlmk/v1 | https://www.protocols.click/view/surgical-procedures-for-simultaneous-optogenetic-m-cv6nw9de | Qianzi Elena He | TITLE: Surgical procedures for simultaneous optogenetic manipulation in the SNc and acute fiber photometry in the dorsal striatum
AUTHORS: Qianzi Elena He
[DESCRIPTION]
This protocol describes the three surgical procedures required for simultaneous optogenetic stimulation in the Substantia Nigra pars compacta (SNc) an... | ["[Viral injection for ChRmine and GRAB-DA3m] Perform unilateral ChRmine and GRAB-DA3m njection following the previous viral injection protocol (https://www.protocols.io/view/midbrain-viral-injections-for-striatal-fiber-photo-5qpvor8zxv4o/v1?step=10step 1-37).", "[Viral injection for ChRmine and GRAB-DA3m] In short, An... |
49,178 | Protocol: Association between visual acuity and subsequent psychotic-like experiences in the Avon Longitudinal Study of Parents and Children | 3 | null | https://www.protocols.io/view/protocol-association-between-visual-acuity-and-sub-bt92nr8e | Natalie Shoham | TITLE: Protocol: Association between visual acuity and subsequent psychotic-like experiences in the Avon Longitudinal Study of Parents and Children
AUTHORS: Natalie Shoham
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a protocol for a planned secondary analysis of longitudinal data, invest... | [] |
55,911 | A three-dimensional immune-oncology model for studying in vitro human NK cell cytotoxic activity | 1 | dx.doi.org/10.17504/protocols.io.b2ufqetn | https://www.protocols.io/view/a-three-dimensional-immune-oncology-model-for-stud-b2ufqetn | Nontaphat Thongsin, Methichit Wattanapanitch | TITLE: A three-dimensional immune-oncology model for studying in vitro human NK cell cytotoxic activity
AUTHORS: Nontaphat Thongsin, Methichit Wattanapanitch
[DESCRIPTION]
Immunotherapy has emerged as a promising therapeutic approach for treating several forms of cancer. Adoptive cell transfer of immune cells, such as... | ["[Isolation and expansion of peripheral blood NK (PB-NK) cells] Isolation of PB-NK cells by negative selection using NK cell isolation kit\n\nWe isolate peripheral blood mononuclear cells (PBMCs) from 30 ml of peripheral blood collected in vacutainer® EDTA blood collection tubes using density gradient centrifugation.\... |
55,393 | Preparation of a reduced Cr2+ solution for sulfide distillation using a Jones Reductor | 6 | dx.doi.org/10.17504/protocols.io.b2b9qar6 | https://www.protocols.io/view/preparation-of-a-reduced-cr2-solution-for-sulfide-b2b9qar6 | Sebastian Rubiano-Rincon, Patrick Larkin | TITLE: Preparation of a reduced Cr2+ solution for sulfide distillation using a Jones Reductor
AUTHORS: Sebastian Rubiano-Rincon, Patrick Larkin
[DESCRIPTION]
This protocol uses a Jones Reductor to prepare reduced Cr2+ for the distillation of H2S from marine sediments. It is an adaptation of a protocol described by Ba... | ["[Jones Reductor Setup and Use] Once set up, the Jones reductor for the reduction of chromium will appear as follows.", "[Jones Reductor Setup and Use] Set up in a support stand a glass-column (~40-cm long, 1.5 cm interior diameter) with an integral sinter at the bottom. Secure a stopcock at the bottom of the column a... |
84,836 | T-5 TICK SHIPPING | 4 | dx.doi.org/10.17504/protocols.io.yxmvm3k36l3p/v1 | https://www.protocols.io/view/t-5-tick-shipping-cw4cxgsw | REDI-NET Consortium | TITLE: T-5 TICK SHIPPING
AUTHORS: REDI-NET Consortium
[DESCRIPTION]
This protocol describes tick shipping.
[GUIDELINES]
OBJECTIVE
To outline steps for proper packaging and shipping of preserved tick samples from a REDI-NET Silver Lab to a REDI-NET Gold Lab.
SUMMARY/SCOPE
The overarching aim of the REDI-NET is to d... | ["[SAMPLE PREPARATION] Primary holding sample holding containers must be leak-proof. Samples should be preserved in appropriate preservative, if applicable (REDI-NET Tick Processing SOP T-2). Ensure that the lids are tightly closed to prevent leaking of storage media while in transit.", "[SAMPLE PREPARATION] Pack vials... |
48,185 | Streptococcal Protein-G and Protein-LG sandwich ELISA | 1 | dx.doi.org/10.17504/protocols.io.btaznif6 | https://www.protocols.io/view/streptococcal-protein-g-and-protein-lg-sandwich-el-btaznif6 | Angel Justiz-Vaillant | TITLE: Streptococcal Protein-G and Protein-LG sandwich ELISA
AUTHORS: Angel Justiz-Vaillant
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This ELISA was used to study the interactions between SpG) and SpLG) with different immunoglobulin preparations from mammalian and avian species. </div></div>
... | ["This ELISA was used to study the interactions between SpG) and SpLG) 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 SpG in carbonate-bicarbonate buffer pH 9.6.", "The plate was then treated with bovine seru... |
49,061 | Thawing Cryopreserved Human Islets | 1 | dx.doi.org/10.17504/protocols.io.bt6dnra6 | https://www.protocols.io/view/thawing-cryopreserved-human-islets-bt6dnra6 | James Lyon, Aliya Spigelman, Jocelyn E Manning Fox, Patrick Macdonald | TITLE: Thawing Cryopreserved Human Islets
AUTHORS: James Lyon, Aliya Spigelman, Jocelyn E Manning Fox, Patrick Macdonald
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol details the thawing of human islets following their cryopreservation, as performed by the Alberta Diabetes Inst... | ["[M199 solution]\nABCDE1M199 (10L)2ReagentConcentrationMass/VolumeSupplierCatalogue #3 M199 powder9.41g/L\n 1 bottle\n Mediatech-Corning90050PB 34 NaHCO326 mM\n 22.0g\n Fisher ScientificS233-5005 HEPES10 mM\n 23.83g\n Fisher ScientificBP310-16 Penicillin/Streptomycin20,000 U/ml penicillin and 20,000 μg/ml streptomycin... |
36,841 | An optimized protocol for in vivo analysis of tumor cell division in a Sleeping Beauty-mediated mouse glioma model. | null | dx.doi.org/10.17504/protocols.io.bf8hjrt6 | https://www.protocols.io/view/an-optimized-protocol-for-in-vivo-analysis-of-tumo-bf8hjrt6 | Maria B Garcia Fabiani, Padma Kadiyala, Pedro R. Lowenstein, Maria G. Castro | TITLE: An optimized protocol for in vivo analysis of tumor cell division in a Sleeping Beauty-mediated mouse glioma model.
AUTHORS: Maria B Garcia Fabiani, Padma Kadiyala, Pedro R. Lowenstein, Maria G. Castro
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS] | [] |
95,765 | PROTEIN LYSATE AND WESTERN BLOT PROTOCOL | 0 | dx.doi.org/10.17504/protocols.io.3byl4qpqjvo5/v1 | https://www.protocols.io/view/protein-lysate-and-western-blot-protocol-c9rvz566 | Scott Vermilyea | TITLE: PROTEIN LYSATE AND WESTERN BLOT PROTOCOL
AUTHORS: Scott Vermilyea
[DESCRIPTION]
This is a collection of protocols including protein lysate preparation in culture, tissue, and immunoblotting (Western) techniques.
[STEPS] | [] |
16,958 | Hybridization and detection of small RNA samples with DIG-labeled probes | null | dx.doi.org/10.17504/protocols.io.us6ewhe | null | Alice Pawlowski | TITLE: Hybridization and detection of small RNA samples with DIG-labeled probes
AUTHORS: Alice Pawlowski
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol can be used to hybridize small RNAs (50 - 200 nt) - either from total RNA isolates or from in vitro transcripts - with digoxigenein-l... | ["[Hybridization]\nprewarm an appropriate volume of DIG Easy Hyb to 62 °C (5 ml per hybridization tube) wet the Northern Blot membrane (9 x 10 cm2 size) in 0.5 x TBE bufferpre-hybridize the membrane with prewarmed DIG Easy Hyb solution in a hybridization tube ( role the membrane with the RNA facing inside) for 30 min a... |
null | null | null | dx.doi.org/10.17504/protocols.io.q4ydyxw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<p>This protocol was designed and developed at this laboratory and incorporates a previously published oligoprobe (see below).</p>
<p>The protocol specifically aims to amplify DENV02 viruses and not other de... | [] |
40,879 | Isolation of Shigella pathogens from oysters | 4 | dx.doi.org/10.17504/protocols.io.bj6pkrdn | https://www.protocols.io/view/isolation-of-shigella-pathogens-from-oysters-bj6pkrdn | Sade Aisha Folashade John, Patrick E. Akpaka, Chandrashekhar Unakal, Arvind Kurhade, Angel Justiz-Vaillant | TITLE: Isolation of Shigella pathogens from oysters
AUTHORS: Sade Aisha Folashade John, Patrick E. Akpaka, Chandrashekhar Unakal, Arvind Kurhade, Angel Justiz-Vaillant
[STEPS]
?. The filtered homogenate was streaked using standardized loops on Salmonella-Shigella (SS) agar, the loops were flamed periodically to ensur... | ["The filtered homogenate was streaked using standardized loops on Salmonella-Shigella (SS) agar, the loops were flamed periodically to ensure sterility. This was done in duplicate. The plates were then incubated at 34°C. After an overnight incubation at 34°C, the plate with the best significant and adequate colonies w... |
107,101 | Using Skimmed milk as a low-cost alternative to IPTG in plasmid expression induction (LacZ Promoter) | 0 | dx.doi.org/10.17504/protocols.io.j8nlk81z6l5r/v1 | https://www.protocols.io/view/using-skimmed-milk-as-a-low-cost-alternative-to-ip-dkt54wq6 | Joseph Shenekji | TITLE: Using Skimmed milk as a low-cost alternative to IPTG in plasmid expression induction (LacZ Promoter)
AUTHORS: Joseph Shenekji
[DESCRIPTION]
This protocol provides a framework for using skimmed milk as an alternative to IPTG for inducing lacZ operon expression in bacteria. Adjustments may be necessary based on ... | ["[process of using Skimmed milk instead of IPTG for induction of protein expression] read the label for the skimmed milk \nit should contain a percentage of carbohydrates (sugars) it is usually 5% for each 100 ml. if you have powdered skimmed milk things are easier, where you can use 1.0% (w/v) of skimmed milk for the... |
32,638 | In Silico Molecular Modeling of the Sodium Iodide Symporter from Homo sapiens | null | dx.doi.org/10.17504/protocols.io.bb46iqze | null | Hristina R. Zhekova, Sergei Y. Noskov | TITLE: In Silico Molecular Modeling of the Sodium Iodide Symporter from Homo sapiens
AUTHORS: Hristina R. Zhekova, Sergei Y. Noskov
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-style:italic;:UNDERLINE;">In Silico</span><span style = ":UNDERLINE;"> Molecular Modeling of the Sod... | [] |
48,721 | SCRINSHOT | 4 | dx.doi.org/10.17504/protocols.io.bttrnnm6 | https://www.protocols.io/view/scrinshot-bttrnnm6 | Alexandros Sountoulidis, Andreas Liontos, Hong Phuong Nguyen, alexandra.firsova , Athanasios Fysikopoulos, Xiaoyan Qian, Werner Seeger, Erik Sundström, Mats Nilsson, christos.samakovlis | TITLE: SCRINSHOT
AUTHORS: Alexandros Sountoulidis, Andreas Liontos, Hong Phuong Nguyen, alexandra.firsova , Athanasios Fysikopoulos, Xiaoyan Qian, Werner Seeger, Erik Sundström, Mats Nilsson, christos.samakovlis
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">SCRINSHOT (Single-Cell Resolution IN Si... | ["[Probe preparation]\nThe genes of interest are selected according to the experimental aims (including optionally a positive control or a house-keeping gene). The SCRINSHOT detection of mRNA is based on a number of steps, for which two types of probes are required: (1) padlock probes to bind specific mRNA sequences an... |
null | null | null | dx.doi.org/10.17504/protocols.io.read3ae | null | null | TITLE: No Title
AUTHORS:
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.nv5de86 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Purpose of this protocol is to introduce plasmid DNA into E. coli cells</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.fnebmbe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Yeast is a well-characterized genome due to its small size and historical significance in genetics. The website http://yeastgenome.org/ is a dedicated resource for yeast genomics.</p>
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
69,415 | Setting a sequencing run with a nanopore MinION and the Rapid Sequencing gDNA kit (SQK-RAD004) | 4 | dx.doi.org/10.17504/protocols.io.4r3l2oy53v1y/v2 | https://www.protocols.io/view/setting-a-sequencing-run-with-a-nanopore-minion-an-cf2ftqbn | Narjol Gonzalez-Escalona | TITLE: Setting a sequencing run with a nanopore MinION and the Rapid Sequencing gDNA kit (SQK-RAD004)
AUTHORS: Narjol Gonzalez-Escalona
[DESCRIPTION]
This protocol is to help in setting up a MinION sequencing run using the rapid sequencing kit from Nanopore (SQK-RAD004). It contains all steps and material needed for a... | ["[Preparation of the DNA Library:] Thaw all reagents in box 1 and 2 of the RAD004 kit.", "[Preparation of the DNA Library:] Take a flow cell from 4-8 °C and leave it at RT.", "[Preparation of the DNA Library:] Prepare the DNA to the suggested concentration of 400 ng total in 7.5 µL, or 54 µL in a 0.2 mL sterile thin-... |
null | null | null | dx.doi.org/10.17504/protocols.io.qnidvce | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Quantitative PCR for amplification of genomic DNA from FFPE (formalin-fixed and paraffin-embedded), PFPE (PAXgene Tissue-fixed and paraffin-embedded), and snap-frozen fixed tissues.</p>
[STEPS]
?. | [] |
71,722 | Lectin C gene analysis | 1 | dx.doi.org/10.17504/protocols.io.x54v9dyk1g3e/v1 | https://www.protocols.io/view/lectin-c-gene-analysis-ciaiuace | Tran Vinh Phuong, Nguyen Ngoc Phuoc, Nguyen Quang Quang Linh | TITLE: Lectin C gene analysis
AUTHORS: Tran Vinh Phuong, Nguyen Ngoc Phuoc, Nguyen Quang Quang Linh
[DESCRIPTION]
Mammalian Tissue Total RNA Purification Protocol by GeneJET RNA Purification Kit (Thermo Scientific, USA)
Before starting:
• Supplement the required amount of Lysis Buffer with β-mercaptoethanol or DTT. A... | ["Mammalian Tissue Total RNA Purification Protocol by GeneJET RNA Purification Kit (Thermo Scientific, USA)", "First Stra nd cDNA Synthesis by RevertAid First Strand cDNA Synthesis kit (Thermo Fisher Scientific, USA)", "PCR products purification by GeneJET Gel Extraction kit (Thermo Scientific, USA)", "Cloning with pG... |
90,722 | HaloTag autophagy flux assay | 4 | dx.doi.org/10.17504/protocols.io.x54v9pwkmg3e/v1 | https://www.protocols.io/view/halotag-autophagy-flux-assay-c4uaywse | Dan Tudorica | TITLE: HaloTag autophagy flux assay
AUTHORS: Dan Tudorica
[DESCRIPTION]
Pule-chaseable method for quantifying autophagy flux
[STEPS]
SECTION: Day 1: Seeding plates
1. Seed 50,000 HeLa cells in each chamber of a 12-well treated tissue culture plate. Maintain cells in DMEM + 10% FBS + 1x Pen-strep.
SECTION: Day 1: Seed... | ["[Day 1: Seeding plates] Seed 50,000 HeLa cells in each chamber of a 12-well treated tissue culture plate. Maintain cells in DMEM + 10% FBS + 1x Pen-strep.", "[Day 1: Seeding plates] Grow for 2 days until cells are ~80% confluent", "[Day 3: Transient Transfection] If cells do not need to be transfected, skip to “day 5... |
6,604 | The method to evaluate antibacterial effect of moth-eye films | 1 | dx.doi.org/10.17504/protocols.io.ipkcdkw | https://www.protocols.io/view/the-method-to-evaluate-antibacterial-effect-of-mot-ipkcdkw | Kiyoshi Minoura | TITLE: The method to evaluate antibacterial effect of moth-eye films
AUTHORS: Kiyoshi Minoura
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This method used a model designed to represent its practical application.</div></div>
[STEPS]
?. [Preparation of microbial suspension]
One colony was selecte... | ["[Preparation of microbial suspension]\nOne colony was selected, inoculated on a new NA plate and cultured again overnight at 37℃", "[Preparation of microbial suspension]\nStaphylococcus aureus (S. aureus) NBRC12732 strain and Esherichia Coli (E. coli) NBRC3972 strain were kindly supplied by the National Institute of ... |
31,486 | Síndrome dos ovários policísticos: suas implicações nos distúrbios metabólicos | null | dx.doi.org/10.17504/protocols.io.bay6ifze | null | Bárbara Karoline Rêgo Beserra Alves, Leandra Caline dos Santos, Antônio Jason Gonçalves da Costa, Maria Rosiany Sousa Moreira, Gleyson Moura dos Santos, Paulo Víctor de Lima e Sousa, Nara Vanessa dos Anjos Barros | TITLE: Síndrome dos ovários policísticos: suas implicações nos distúrbios metabólicos
AUTHORS: Bárbara Karoline Rêgo Beserra Alves, Leandra Caline dos Santos, Antônio Jason Gonçalves da Costa, Maria Rosiany Sousa Moreira, Gleyson Moura dos Santos, Paulo Víctor de Lima e Sousa, Nara Vanessa dos Anjos Barros
[DESCRIPTI... | [] |
105,064 | Optimized Cloning Protocol for Standard Curve Generation in qPCR of Environmental Functional Genes | 0 | dx.doi.org/10.17504/protocols.io.5qpvok2odl4o/v1 | https://www.protocols.io/view/optimized-cloning-protocol-for-standard-curve-gene-diug4etw | Abul Bashar, Raju Podduturi, Amaru Miranda Djurhuus, H. M. Rakibul Islam, Mohammad Mahfujul Haque, Lars Hestbjerg Hansen, Niels O. G. Jørgensen | TITLE: Optimized Cloning Protocol for Standard Curve Generation in qPCR of Environmental Functional Genes
AUTHORS: Abul Bashar, Raju Podduturi, Amaru Miranda Djurhuus, H. M. Rakibul Islam, Mohammad Mahfujul Haque, Lars Hestbjerg Hansen, Niels O. G. Jørgensen
[DESCRIPTION]
Due to the complex and varied biochemical requ... | ["[Step-1: Amplification of Target Gene Sequence] Amplify the target gene sequences from environmental DNA using a PCR reaction. The reaction mixture should include polymerase (0.5 μL), buffer (5 μL), dNTPs (5 μL), forward primer (1 μL), reverse primer (1 μL), template DNA (3 μL), and water (32.5 μL).\n \nNote: The pr... |
86,174 | iNDI PiggyBac-TO-hNGN2 transfection protocol Version 1 | 4 | dx.doi.org/10.17504/protocols.io.rm7vzxb22gx1/v1 | https://www.protocols.io/view/indi-piggybac-to-hngn2-transfection-protocol-versi-cyd6xs9e | Mark Cookson, michael.ward, Erika Lara Flores | TITLE: iNDI PiggyBac-TO-hNGN2 transfection protocol Version 1
AUTHORS: Mark Cookson, michael.ward, Erika Lara Flores
[DESCRIPTION]
PiggyBac Method for hNGN2 transfection
Transfection protocol
Use of CEPT: Nature Methods 18, 528-541, 2021
[STEPS]
SECTION: Transfection protocol
1. Observe KOLF2.1 iPSCs under a phase co... | ["[Transfection protocol] Observe KOLF2.1 iPSCs under a phase contrast microscope to assess confluency and presence of cells debris. Dish should be dissociated at ~70% to 90% confluency.\n\nCoat a well of 6 well plate to be used for transfection with 1 mL of Matrigel solution, tilting to ensure coverage of entire surfa... |
32,883 | Relationship of vancomycin trough levels with acute kidney injury risk: an exposure-toxicity meta-analysis | null | dx.doi.org/10.17504/protocols.io.bcctiswn | null | Ioannis Bellos, Georgios Daskalakis, Vasilios Pergialiotis | TITLE: Relationship of vancomycin trough levels with acute kidney injury risk: an exposure-toxicity meta-analysis
AUTHORS: Ioannis Bellos, Georgios Daskalakis, Vasilios Pergialiotis
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Vancomycin is a tricyclic glycopeptide antimicrobial agent with activ... | ["Review title: Relationship of vancomycin trough levels with acute kidney injury risk: an exposure-toxicity meta-analysis", "Review question: The meta-analysis aims to clarify whether higher vancomycin trough levels are linked to increased acute kidney injury risk and define an exposure-response relationship between t... |
null | null | null | dx.doi.org/10.17504/protocols.io.muqc6vw | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocal for eye movment biometric recognition</p>
[STEPS]
?.
?.
?.
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.es7behn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
68,692 | Generation of stable cell lines via retroviral or lentiviral transduction | 1 | dx.doi.org/10.17504/protocols.io.kqdg3prxpl25/v1 | https://www.protocols.io/view/generation-of-stable-cell-lines-via-retroviral-or-cfbutinw | Rotimi Fasimoye, Dario R Alessi | TITLE: Generation of stable cell lines via retroviral or lentiviral transduction
AUTHORS: Rotimi Fasimoye, Dario R Alessi
[DESCRIPTION]
The ability to stably express a protein of interest in cells is critical to study its function. Here, we describe a protocol to generate stable cell lines using a retrovirus system th... | ["[Packaging SLC35A2-2xFLAG plasmid into a Retrovirus system] Grow HEK293FT cells to 50-60% confluency in Growth media in a Petri Dish.", "[Packaging SLC35A2-2xFLAG plasmid into a Retrovirus system] Prepare a transfection mix in a sterile 1.5 ml Eppendorf tube, containing:\n\n3.8 µg pGag/Pol plasmid\n2.2 µg pVSVG pla... |
66,616 | SonoVive Reviews – Does This Advanced Ear Health Formula Enhance Your Hearing? | 3 | dx.doi.org/10.17504/protocols.io.5qpvob6wdl4o/v1 | https://www.protocols.io/view/sonovive-reviews-does-this-advanced-ear-health-for-cdays2fw | Sonovive | TITLE: SonoVive Reviews – Does This Advanced Ear Health Formula Enhance Your Hearing?
AUTHORS: Sonovive
[DESCRIPTION]
SonoVive Reviews is a viable high-level hearing well-being recipe that advances hearing well-being and supports mind capability. This supplement turns out successfully for anybody at whatever stage ... | [] |
42,554 | Public protocol | 1 | dx.doi.org/10.17504/protocols.io.bms2k6ge | https://www.protocols.io/view/public-protocol-bms2k6ge | Monica Hassan Bonita Espadrilla | TITLE: Public protocol
AUTHORS: Monica Hassan Bonita Espadrilla
[STEPS] | [] |
69,652 | Molecular Observatory Network (MONet) | 2 | dx.doi.org/10.17504/protocols.io.5jyl8jr49g2w/v1 | https://www.protocols.io/view/molecular-observatory-network-monet-cf9utr6w | maggie.bowman, Alexis Heath, Tamas Varga, Anil Battu, Will Kew, Cheng Shi, Rosey Chu, Che Clendinen, Jason.Toyoda, Odeta Qafoku, qian.zhao, izabel.stohel, Rey Hauchambe, Michael Rosenstock, Albert Lawver, nicholas.sconzo, James Anderson, Patricia Miller, andrew.townsend, Nancy Hess, John Bargar, emily.graham | TITLE: Molecular Observatory Network (MONet)
AUTHORS: maggie.bowman, Alexis Heath, Tamas Varga, Anil Battu, Will Kew, Cheng Shi, Rosey Chu, Che Clendinen, Jason.Toyoda, Odeta Qafoku, qian.zhao, izabel.stohel, Rey Hauchambe, Michael Rosenstock, Albert Lawver, nicholas.sconzo, James Anderson, Patricia Miller, andrew.town... | [] |
13,935 | Zebrafish (Danio rerio) Environmental Summary, LaNeC (Marabá/PA, Brazil) | null | dx.doi.org/10.17504/protocols.io.rupd6vn | null | Caio Maximino, Monica Gomes Lima-Maximino, Diógenes Silva | TITLE: Zebrafish (Danio rerio) Environmental Summary, LaNeC (Marabá/PA, Brazil)
AUTHORS: Caio Maximino, Monica Gomes Lima-Maximino, Diógenes Silva
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Environmental and housing conditions experienced by laboratory animals exert profound effects on th... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.exubfnw | null | null | TITLE: No Title
AUTHORS:
[GUIDELINES]
<strong>Materials:</strong><br />• Sterile PBS <br />• Anti-mouse CD3ε, clone 145-2C11 (LEAF™ format, Cat. No. 100313/100314; Ultra-LEAF™ format, Cat. No. 100339/100340) <br />• Cell culture medium (e.g., RPMI-1640 or IMDM supplemented with 10% FBS and 2mM L-glutamine) <br />• St... | [] |
104,413 | Home made SM 100bp DNA ladder for agarose gel | 0 | dx.doi.org/10.17504/protocols.io.dm6gpz535lzp/v1 | https://www.protocols.io/view/home-made-sm-100bp-dna-ladder-for-agarose-gel-dh7539q6 | Stéphane Mauger | TITLE: Home made SM 100bp DNA ladder for agarose gel
AUTHORS: Stéphane Mauger
[DESCRIPTION]
The SM 100pb DNA Ladder is a standard size marker equivalent to the Fisher’s O'RangeRuler‱ 100 pb DNA Ladder (#SM0623). The SM 100pb Ladder allows to determine the size of double-stranded DNA fragments between 100 bp and 1500 b... | ["[Primers and pGEM®-3Zf(+) Vectors preparation] Oligo primers dilution\nin 16 1.5 mL microtubes, dilute 1:10 each oligo primer at 100µM to final concentration 10µM, see the SM100pb_primers.xlsx file below.\n50 µL oligo primer (100µM)\n450 µL nuclease free water \n\nHomogenize and store at 4 °C (or at -20 °C for a l... |
25,306 | Hornwort growth media | null | dx.doi.org/10.17504/protocols.io.4x2gxqe | null | Eftychis Frangedakis | TITLE: Hornwort growth media
AUTHORS: Eftychis Frangedakis
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Hornworts have a remarkable regenerative capacity. For tissue culturing / propagation you just need to transfer a small tissue fragment on fresh media and that's it... it will keep growing.</d... | ["Using a sterile scalpel tranfer a small thallus tissue fragment (around 3mm x 3mm, but can also be smaller or bigger) on KNOP or BCD fresh media plates. Grow at 21oC, 12 h of light and 12 h of dark, 1500 lux light intensity", "Subculture every 1-2 months"] |
85,939 | AT8 Tau Pathology Image Analysis | 1 | dx.doi.org/10.17504/protocols.io.n2bvj386wlk5/v1 | https://www.protocols.io/view/at8-tau-pathology-image-analysis-cx6txren | Hemanth Ramesh Nelvagal, Toby J Curless, Zane Jaunmuktane | TITLE: AT8 Tau Pathology Image Analysis
AUTHORS: Hemanth Ramesh Nelvagal, Toby J Curless, Zane Jaunmuktane
[DESCRIPTION]
QuPath is a bioimage analysis software designed for digital pathology and whole slide image analysis. This protocol describes how to analyse AT8 tau pathology in human brain tissue (FFPE sections wi... | ["[Annotation] Manually annotate regions of interest on NZConnect (Hamamatsu), a web-based whole-slide image (WSI) viewer:https://www.hamamatsu.com/us/en/product/life-science-and-medical-systems/digital-slide-scanner/U16179-01.html.", "[Annotation] Download annotations using a Python script.", "[QuPath De-Convolution a... |
null | null | null | dx.doi.org/10.17504/protocols.io.dbf2jm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
Similar to YPD Medium for budding yeast, YES Medium is the rich growth medium utilized for fission yeast.
[STEPS]
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?.
?. | [] |
24,080 | Agro Preparation for Mimulus in Planta Transformation | null | dx.doi.org/10.17504/protocols.io.3rqgm5w | null | Yaowu Yuan | TITLE: Agro Preparation for Mimulus in Planta Transformation
AUTHORS: Yaowu Yuan
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol is part of a </span><a style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">collection for </span><span style = ":;font-st... | ["Inoculate 4 agro colonies into separate tubes of LB+Kan+Gent+Rif.\n5 ml", "Colony PCR from the 5 mL culture to check that it has your insert.", "Inoculate correct agro colony into a flask of LB+Kan+Gent+Rif, and cover with foil.\n300 ml", "Make glycerol stocks by adding of agro to glycerol stock tube.\n1 ml", "Tra... |
57,166 | RNA extraction from colonial tunicates | 4 | dx.doi.org/10.17504/protocols.io.b33nqqme | https://www.protocols.io/view/rna-extraction-from-colonial-tunicates-b33nqqme | Marta Wawrzyniak, Simon Blanchoud | TITLE: RNA extraction from colonial tunicates
AUTHORS: Marta Wawrzyniak, Simon Blanchoud
[DESCRIPTION]
This protocol has been successfully used with Botrylloides diegensis and has been adapted from the following publication:
An efficient low-cost laboratory workflow for the study of blood cells and RNA extraction... | ["Clean the slide from which you will take the colony of your interest. See Cleaning colonial ascidians.", "Isolate a cleaned colony composed of approx. 20 zooids.", "Transfer to a tube and spin at maximum speed for 2 min .", "Remove the excess water and shock-freeze the tube in liquid nitrogen.", "Add 400 µL of extrac... |
null | null | null | dx.doi.org/10.17504/protocols.io.d6p9dm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This tutorial explains how to use VIROME to discover novel genetic polymorphism from viral metagenome shotgun data. <br /><br />Wommack, K. E., J. Bhavsar, S. W. Polson, J. Chen, M. Dumas, S. Srinivasiah, M. Furman, S. Jamindar, and D. J. Nasko. 2012. VIROME: a standard operatin... | [] |
71,864 | Protocols for processing of fresh murine tissues for flow cytometry | 4 | dx.doi.org/10.17504/protocols.io.5qpvorb49v4o/v1 | https://www.protocols.io/view/protocols-for-processing-of-fresh-murine-tissues-f-cieyubfw | Diana Rose E Ranoa | TITLE: Protocols for processing of fresh murine tissues for flow cytometry
AUTHORS: Diana Rose E Ranoa
[DESCRIPTION]
To assess the immune cell composition immediately after 237 CAR treatment, we performed immunophenotyping by flow cytometry on samples from blood, spleen, pancreas, and ascites fluid recovered from ID8C... | ["Whole blood collected using heparinized capillary tubes (~70uL)", "Incubate with 2mL of 1X ACK lysis buffer for 10 minutes then add 2mL RPMI+5%FBS", "Centrifuge at 350xg for 5 minutes", "Wash with 1mL PBS + 0.5% BSA buffer, then centrifuge at 350xg for 5 minutes. Perform twice.", "Resuspend cells in 0.5mL PBS + 0.5% ... |
57,911 | Freely moving recording: Chronic recoverable Neuropixels in mice | 1 | null | https://www.protocols.io/view/freely-moving-recording-chronic-recoverable-neurop-b4sxqwfn | Emily A Aery Jones | TITLE: Freely moving recording: Chronic recoverable Neuropixels in mice
AUTHORS: Emily A Aery Jones
[DESCRIPTION]
This protocol collection explains how to build a low-cost, lightweight system to implant Neuropixels 1.0 probes into mice, record during freely moving behavior, then recover the probe for future use. This ... | ["[Design the enclosure] Consider what acrylic to use (e.g. 1/4\" P95 matte black acrylic).\nUse black if you're planning to track LEDs in the dark or white if you're planning to track a Black6 mouse based on center of mass.\nUse matte finish to reduce reflections from LEDs and overhead lights.\nThicker material makes ... |
32,194 | Assessment of safety and effectiveness for pediatric patients of cryoanalgesia compared to epidural for the Nuss procedure in real-world data from Electronic Health Records: a protocol and statistical analysis plan | null | dx.doi.org/10.17504/protocols.io.bbpaimie | null | Benjamin S. Glicksberg, Roberto Mora, Stefano Rensi, Vivek A. Rudrapatna, Andrew M. Bishara, Elizabeth Gress, Rohit Vashisht, Michael Zobel, Benjamin Padilla, Benjamin Padilla, Atul J. Butte | TITLE: Assessment of safety and effectiveness for pediatric patients of cryoanalgesia compared to epidural for the Nuss procedure in real-world data from Electronic Health Records: a protocol and statistical analysis plan
AUTHORS: Benjamin S. Glicksberg, Roberto Mora, Stefano Rensi, Vivek A. Rudrapatna, Andrew M. Bisha... | ["[cohort Identification]\nNuss procedure", "[Cohort Identification of Nuss Procedure]\nThe pediatric surgical department provided a list of medical record numbers of all patients that underwent a Nuss procedure. We will only analyze data for patients that were under 22 years of age (i.e., pediatric population) at the ... |
78,229 | Ussing chamber experiments for distension evoked secretion in mucosa/submucosa preparations from human colon | 1 | dx.doi.org/10.17504/protocols.io.8epv5joqdl1b/v1 | https://www.protocols.io/view/ussing-chamber-experiments-for-distension-evoked-s-cqmvvu66 | Klaus Michel, Stefanie Schäuffele, Michael Schemann, Gemma Mazzuoli-Weber | TITLE: Ussing chamber experiments for distension evoked secretion in mucosa/submucosa preparations from human colon
AUTHORS: Klaus Michel, Stefanie Schäuffele, Michael Schemann, Gemma Mazzuoli-Weber
[DESCRIPTION]
This protocol is to investigate the mechanisms of mechanically induced secretion in human colon. For this... | ["Samples of human colon were placed in ice-cold oxygenated Krebs solution and washed by gentle agitation. Tissues were then dissected in fresh ice-cold oxygenated Krebs solution to obtain preparations containing the mucosa and all submucosal plexi.", "Tissue samples were cut into pieces of 1cm² or 0.5cm² and mounted i... |
36,655 | SPARC Cat acute UroMOCA implantation surgery | 1 | dx.doi.org/10.17504/protocols.io.bf2pjqdn | https://www.protocols.io/view/sparc-cat-acute-uromoca-implantation-surgery-bf2pjqdn | Brett Hanzlicek, Ben Abelson, Margot Damaser, Dennis Bourbeau | TITLE: SPARC Cat acute UroMOCA implantation surgery
AUTHORS: Brett Hanzlicek, Ben Abelson, Margot Damaser, Dennis Bourbeau
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol for cat surgery to expose the badder for inactive device insertion.</div></div>
[STEPS]
?. [Animal Prep and cathe... | ["[Animal Prep and catheter placement]\nCat is anesthetized and abdomen is shaved by the Cleveland Clinic vet team. The cat is then moved into the surgery room and attached to monitors by the vet team.", "[Animal Prep and catheter placement]\nDrape cat and perform betadine scrub on abdomen and genitals.", "[Animal Pre... |
34,403 | Illuminated Orbital Shaker for Microalgae Culture | null | dx.doi.org/10.17504/protocols.io.bdubi6sn | null | Jakub Nedbal | TITLE: Illuminated Orbital Shaker for Microalgae Culture
AUTHORS: Jakub Nedbal
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Microalgae are grown for the research on photosynthesis, biotechnology, and water-environment ecology. Specialized laboratories typically use calibrated commercial equ... | ["The components for the algal shaker can be sourced from four types of suppliers.Laboratory equipment supplierElectronics parts distributorPrinted circuit board manufacturer3D printing service (or in-house 3D printer)The orbital shaker can be sourced from laboratory equipment suppliers. The orbital shaker described in... |
104,926 | Behavioral analyses in mice | 0 | dx.doi.org/10.17504/protocols.io.rm7vzj234lx1/v1 | https://www.protocols.io/view/behavioral-analyses-in-mice-dip64dre | Nicolas Giguère, louis-eric.trudeau Trudeau | TITLE: Behavioral analyses in mice
AUTHORS: Nicolas Giguère, louis-eric.trudeau Trudeau
[DESCRIPTION]
This collection of protocols describes different behavioural assays performed in mice including, grip strength test, pole test, rotarod, open field and nose poking learning task.
[GUIDELINES]
This protocol needs pri... | ["[Grip strength test] A grip strength apparatus (BioSeb instruments, BIO-GS3, France) was used to evaluate paw force of 10-12-week-old male or female mice.\n\nProcedure:", "[Grip strength test] Habituate the mouse in the testing room for at least 60 min.", "[Grip strength test] Hold the mouse firmly by the tail and sl... |
49,252 | Assessing multiplex tiling PCR sequencing approaches for detecting genomic variants of SARS-CoV-2 in municipal wastewater | 1 | dx.doi.org/10.17504/protocols.io.buccnssw | https://www.protocols.io/view/assessing-multiplex-tiling-pcr-sequencing-approach-buccnssw | Xuan Lin, Melissa Glier, Kevin Kuchinski, Tenysha Ross-Van Mierlo, David McVea, John Tyson, Natalie Prystajecky, Ryan Ziels | TITLE: Assessing multiplex tiling PCR sequencing approaches for detecting genomic variants of SARS-CoV-2 in municipal wastewater
AUTHORS: Xuan Lin, Melissa Glier, Kevin Kuchinski, Tenysha Ross-Van Mierlo, David McVea, John Tyson, Natalie Prystajecky, Ryan Ziels
[DESCRIPTION]
<div class = "text-blocks"><div class = "t... | ["[First strand cDNA synthesis]\nPreparation of master mix", "[First strand cDNA synthesis]\nPrepare the following components in a 1.5 mL Eppendorf DNA LoBind tube for the number of samples that will be tested and dispense to 0.2mL each PCR tubes. Briefly spin down the 0.2 mL tubes containing Master Mix RT_1 and keep ... |
101,962 | A selective process for application of EDC and 4-APEBA for carbonyl containing metabolites by MALDI-MSI | 0 | dx.doi.org/10.17504/protocols.io.ewov19d9ylr2/v2 | https://www.protocols.io/view/a-selective-process-for-application-of-edc-and-4-a-dfti3nke | Kevin J Zemaitis, Christopher R Anderton, Dusan Velickovic | TITLE: A selective process for application of EDC and 4-APEBA for carbonyl containing metabolites by MALDI-MSI
AUTHORS: Kevin J Zemaitis, Christopher R Anderton, Dusan Velickovic
[DESCRIPTION]
Herein, we outline the protocol for application of 4-(2-((4-bromophenethyl)dimethylammonium)ethoxy)benzenaminium dibromide (4-... | ["[Materials for OTCD] All chemicals were used as received without any further purification, and synthesis of 4-APEBA was completed in house:\n\n1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) hydrochloride - CAS Number: 25952-53-8 - Sigma-Aldrich (>98.0%; St. Louis, MO) or Tokyo Chemical Industry Co. (>98.0%; Port... |
67,368 | TRUFLEXEN – A PROMISING LIFE TO YOUR HEALTH AND FITNESS | 3 | dx.doi.org/10.17504/protocols.io.kqdg3pzrel25/v1 | https://www.protocols.io/view/truflexen-a-promising-life-to-your-health-and-fitn-cd2gs8bw | xojifov , truflexenmuscleus | TITLE: TRUFLEXEN – A PROMISING LIFE TO YOUR HEALTH AND FITNESS
AUTHORS: xojifov , truflexenmuscleus
[DESCRIPTION]
Truflexen
[STEPS] | [] |
16,847 | High molecular weight DNA extraction for long read sequencing | null | dx.doi.org/10.17504/protocols.io.uppevmn | null | Karen Cristine Gonçalves dos Santos, Megan McDonald | TITLE: High molecular weight DNA extraction for long read sequencing
AUTHORS: Karen Cristine Gonçalves dos Santos, Megan McDonald
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Adaptation of the protocol </span><a style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":... | ["[Extraction]\n2.5 volume of Buffer A 5 mL2.5 volume of Buffer B 5 mL1.0 volume of Buffer C 2 mLPVP 40 10% 1mLPVP 10 10% 1mL\nThis protocol is an adaptation from https://www.protocols.io/view/high-quality-dna-from-fungi-for-long-read-sequenci-k6qczdw", "[Extraction]\nGrind tissue/spores... |
94,598 | Purification of recombinant Low Density Lipoprotein Receptor Related Protein Associated Protein 1 (LRPAP1, RAP) from Escherichia coli | 1 | dx.doi.org/10.17504/protocols.io.rm7vzxpb2gx1/v1 | https://www.protocols.io/view/purification-of-recombinant-low-density-lipoprotei-c8mezu3e | Patricia Yuste-Checa, Silvia Gärtner, F Ulrich Hartl | TITLE: Purification of recombinant Low Density Lipoprotein Receptor Related Protein Associated Protein 1 (LRPAP1, RAP) from Escherichia coli
AUTHORS: Patricia Yuste-Checa, Silvia Gärtner, F Ulrich Hartl
[DESCRIPTION]
This protocol details how to efficiently purify LDL Receptor Related Protein Associated Protein 1 (LRP... | ["[LRPAP1 express4ion] Thaw RbCl-competent Escherichia coli Bl21 cells (DE3) on ice.", "[LRPAP1 express4ion] Add 1 µL of pQTEV-LRPAP1 plasmid without the signal peptide (1-35 amino acids) and incubate 30 min on ice.", "[LRPAP1 express4ion] Heat shock 45 s at 42 °C.", "[LRPAP1 express4ion] Incubate on ice 2 min, then ad... |
88,327 | Evaluation of point-of-use treatments and biochar to reduce 1,2,3-trichloropropane (TCP) contamination in drinking water | 6 | dx.doi.org/10.17504/protocols.io.14egn3496l5d/v1 | https://www.protocols.io/view/evaluation-of-point-of-use-treatments-and-biochar-c2hfyb3n | B Hope Hauptman, Colleen C Naughton | TITLE: Evaluation of point-of-use treatments and biochar to reduce 1,2,3-trichloropropane (TCP) contamination in drinking water
AUTHORS: B Hope Hauptman, Colleen C Naughton
[DESCRIPTION]
In this study, we explore the potential of commercially available off-the-shelf pitcher point-of-use filters for reducing TCP levels... | ["[Section 1: General information] General\nProcedures were performed at room temperature at approximately 20 °C (the recorded temperature was 21.5oC). \nSamples collected for GC-MS testing at BSK Analytical Laboratories in Fresno, California were held at 4oC for a maximum of 4 days before being transported on ice fo... |
35,080 | Site-directed mutagenesis | null | dx.doi.org/10.17504/protocols.io.behgjb3w | null | Johannes Stuttmann | TITLE: Site-directed mutagenesis
AUTHORS: Johannes Stuttmann
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Site-directed mutagenesis (SDM) as described here is used to introduce a mutation in the sequence of a plasmid of interest by PCR-based methods. Several different approaches have been p... | [] |
82,039 | Run Clearmap 2 docker | 5 | dx.doi.org/10.17504/protocols.io.yxmvmn9pbg3p/v3 | https://www.protocols.io/view/run-clearmap-2-docker-cucxwsxn | Moritz Negwer | TITLE: Run Clearmap 2 docker
AUTHORS: Moritz Negwer
[DESCRIPTION]
This protocol is a supplement to our upcoming publication "FriendlyClearMap: An optimized toolkit for mouse brain mapping and analysis".
In this protocol, we describe in detail how to run Clearmap2's CellMap portion in a Docker container.
[STEPS]
SE... | ["[Docker Setup] On Windows: \nIf you haven't already, download and set up Docker Desktop for Windows. This requires administrator privileges and will also install the Windows Subsystem for Linux (WSL2). \n\nDownload: \nhttps://www.docker.com/products/docker-desktop \n\nAlternatively, use our install script via powersh... |
40,426 | University College Dublin (UCD) Zebrafish Facility Environmental Parameters: 2019 | 3 | dx.doi.org/10.17504/protocols.io.bjqikmue | https://www.protocols.io/view/university-college-dublin-ucd-zebrafish-facility-e-bjqikmue | Grace Kennedy, Husvinee Sundaramurthi, UCD Biomedical Facility Staff , Breandán Kennedy | TITLE: University College Dublin (UCD) Zebrafish Facility Environmental Parameters: 2019
AUTHORS: Grace Kennedy, Husvinee Sundaramurthi, UCD Biomedical Facility Staff , Breandán Kennedy
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify"><span>Environ... | [] |
43,283 | Dundee neutrophil isolation protocol (from whole blood) | 4 | dx.doi.org/10.17504/protocols.io.bnhtmb6n | https://www.protocols.io/view/dundee-neutrophil-isolation-protocol-from-whole-bl-bnhtmb6n | Ying Fan, Andrew J.M. Howden, Dario R. Alessi, Esther M. Sammler | TITLE: Dundee neutrophil isolation protocol (from whole blood)
AUTHORS: Ying Fan, Andrew J.M. Howden, Dario R. Alessi, Esther M. Sammler
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify">We describe a fast and efficient immunomagnetic negative isolat... | ["Collect into BD Vacutainer. Ensure is collected by not prematurely discontinuing blood collection. Mix gently by inverting tubes 7-8 times.\n[blood]\n[blood]", "Transfer into a 50 mL falcon tube.\n[blood]", "Add to blood . Mix gently.\n[“EDTA Stock Solution 1” (0.1M EDTA-PBS solution)]", "Add from the neutrophil ... |
77,298 | Active Absorption of Glucose in the Small Intestine | 1 | dx.doi.org/10.17504/protocols.io.rm7vzb2yrvx1/v1 | https://www.protocols.io/view/active-absorption-of-glucose-in-the-small-intestin-cpqsvmwe | Biolprocess | TITLE: Active Absorption of Glucose in the Small Intestine
AUTHORS: Biolprocess
[DESCRIPTION]
This is the protocol for the active absorption of glucose from within the small intestine. This process allows for the absorption of glucose at low concentrations.
[STEPS]
SECTION: Active Absorption of Glucose in the Small ... | ["[Active Absorption of Glucose in the Small Intestine] When the concentration gradient between the blood and the ileum is low, active methods may be used to absorb glucose into the blood", "[Active Absorption of Glucose in the Small Intestine] Co-transport proteins in the cell membranes of the cells lining the ileum",... |
63,887 | INTRAMUSCULAR PFF INJECTION PROTOCOL | 4 | dx.doi.org/10.17504/protocols.io.n2bvj6j75lk5/v1 | https://www.protocols.io/view/intramuscular-pff-injection-protocol-campsc5n | LEE LAB RESEARCH LABORATORY, Michael Lee | TITLE: INTRAMUSCULAR PFF INJECTION PROTOCOL
AUTHORS: LEE LAB RESEARCH LABORATORY, Michael Lee
[DESCRIPTION]
This protocol details the intramuscular PFF injection procedure.
[STEPS]
SECTION: Procedure
1. Clean the procedure hood.
SECTION: Procedure
2. Turn on the heating pad and cover it with a blue procedure pad.
SEC... | ["[Procedure] Clean the procedure hood.", "[Procedure] Turn on the heating pad and cover it with a blue procedure pad.", "[Procedure] Connect dental needle with tubing.", "[Procedure] Fill up PBS into the tubing using a small syringe.", "[Procedure] Insert the Hamilton Syringe into the tube for 2-3 mm.", "[Procedure] C... |
35,624 | Slice Preparation and Blockface Imaging for Electrophysiology - Mouse | null | dx.doi.org/10.17504/protocols.io.be2gjgbw | null | Allen Institute for Brain Science | TITLE: Slice Preparation and Blockface Imaging for Electrophysiology - Mouse
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the procedure for transcardial perfusion of an adult mouse, followed by dissection, embedding, slicing, and ... | [] |
101,107 | Purification of NIX-GST | 0 | dx.doi.org/10.17504/protocols.io.q26g711dkgwz/v1 | https://www.protocols.io/view/purification-of-nix-gst-deyt3fwn | Elias Adriaenssens | TITLE: Purification of NIX-GST
AUTHORS: Elias Adriaenssens
[DESCRIPTION]
This protocol details the purification of NIX-GST.
[STEPS]
SECTION: Purification
1. To purify NIX-GST, fuse the cytosol-exposed domain of NIX (1-182aa) to a C-terminal GST-tag through cloning into a pET-DUET1 vector (available from Addgene).
SE... | ["[Purification] To purify NIX-GST, fuse the cytosol-exposed domain of NIX (1-182aa) to a C-terminal GST-tag through cloning into a pET-DUET1 vector (available from Addgene).", "[Purification] Introduce the point mutants in vitro mutagenesis to generate NIX E72A/L75A/D77A/E81A (4A; ΔWIPI2) (available from Addgene), and... |
79,016 | Mo'orea Coastal Use Monitoring Protocol | 1 | dx.doi.org/10.17504/protocols.io.5qpvor1b9v4o/v1 | https://www.protocols.io/view/mo-39-orea-coastal-use-monitoring-protocol-cregv3bw | Ellis Gelt, Grace Sandel, Kiran Bengard, Laura Barragan, slicata, Ellinor Arzbaecher, jparadise, Juliet Capriola | TITLE: Mo'orea Coastal Use Monitoring Protocol
AUTHORS: Ellis Gelt, Grace Sandel, Kiran Bengard, Laura Barragan, slicata, Ellinor Arzbaecher, jparadise, Juliet Capriola
[DESCRIPTION]
This procedure is used for costal monitoring and has been tested along the majority of the coast of Mo'orea, French Polynesia; comp... | ["[GAIA GPS Tracking] Have two team-members start a track on GAIA GPS. Make sure both members have full battery.", "[Birds] When you see a bird, record the number and identify whether the bird(s) is an egret or heron. Refer to the bird ID sheet, linked here.", "[Birds] Record the timestamp at the time you spotted the b... |
90,920 | RSVAB WGS and GF protocols | 1 | dx.doi.org/10.17504/protocols.io.kqdg3xbzqg25/v1 | https://www.protocols.io/view/rsvab-wgs-and-gf-protocols-c42gyybw | miglesias | TITLE: RSVAB WGS and GF protocols
AUTHORS: miglesias
[DESCRIPTION]
This SOP describes the procedure for generating cDNA from RSV viral nucleic acid extracts and subsequently producing amplicons tiling the viral genome using. We propose two systems for genomic characterization of RSV. First, a novel RSV amplicon-based ... | ["[dsCDNA generation:] During this step three master mixes will be prepared: MMI, MMII and MMIII.\nMaterials: Kit Superscript III First Strand (Invitrogen)\n 100% DMSO\n RNAseH (Invitrogen)\n Klenow fragment 3' ->5' exo (New England Biolab... |
35,918 | Associations of antithrombotic agent use with clinical outcomes in critically ill patients with troponin I elevation in the absence of acute coronary syndrome (Table 6) | null | dx.doi.org/10.17504/protocols.io.bfbnjime | https://www.protocols.io/view/associations-of-antithrombotic-agent-use-with-clin-bfbnjime | Chuan-Tsai Tsai, Ya-Wen Lu, Ruey-Hsing Chou, Yi-Lin Tsai, Ming-Ren Kuo, Jiun-Yu Guo, Chi-Ting Lu, Chin-Sung Kuo, Po-Hsun Huang | TITLE: Associations of antithrombotic agent use with clinical outcomes in critically ill patients with troponin I elevation in the absence of acute coronary syndrome (Table 6)
AUTHORS: Chuan-Tsai Tsai, Ya-Wen Lu, Ruey-Hsing Chou, Yi-Lin Tsai, Ming-Ren Kuo, Jiun-Yu Guo, Chi-Ting Lu, Chin-Sung Kuo, Po-Hsun Huang
[DESCRI... | [] |
108,675 | Protocol for a scoping review to map the evidence around laboratory tests for use in low resources settings | 0 | dx.doi.org/10.17504/protocols.io.14egn6krzl5d/v1 | https://www.protocols.io/view/protocol-for-a-scoping-review-to-map-the-evidence-dndb5a2n | Virginie Viprey, Kerrie Davies, Jane Freeman, Robyn Meurant, Mike Messenger | TITLE: Protocol for a scoping review to map the evidence around laboratory tests for use in low resources settings
AUTHORS: Virginie Viprey, Kerrie Davies, Jane Freeman, Robyn Meurant, Mike Messenger
[DESCRIPTION]
The aim of this thematic evidence review is to identify and provide
guidance on the application of differ... | [] |
87,393 | Sanger Tree of Life HMW DNA Extraction: Automated Plant MagAttract v.3 | 4 | dx.doi.org/10.17504/protocols.io.ewov1q9k2gr2/v1 | https://www.protocols.io/view/sanger-tree-of-life-hmw-dna-extraction-automated-p-czj9x4r6 | graeme oatley, Amy Denton, Caroline Howard | TITLE: Sanger Tree of Life HMW DNA Extraction: Automated Plant MagAttract v.3
AUTHORS: graeme oatley, Amy Denton, Caroline Howard
[DESCRIPTION]
This protocol describes the automated extraction and SPRI of HMW DNA from cryogenically homogenised plant and fungi tissue samples that are intended for long-read sequencing. ... | ["[Sample lysis] Prepare a lysis buffer master mix:\n \n ReagentVolume per samplePhosphate buffered saline (PBS)200 µLProteinase K20 µLRNase A4 µLBuffer AL150 µL", "[Sample lysis] Set a heat block to 55 °C.", "[Sample lysis] Transfer 50 mg of cryogenically homogenised tissue from each sample to 2 mL microcentrifuge tu... |
91,848 | Immunofluorescence of ATP13A2 and CD63 | 1 | dx.doi.org/10.17504/protocols.io.bp2l6xy3klqe/v1 | https://www.protocols.io/view/immunofluorescence-of-atp13a2-and-cd63-c5xgy7jw | Stephanie Vrijsen, Peter Vangheluwe | TITLE: Immunofluorescence of ATP13A2 and CD63
AUTHORS: Stephanie Vrijsen, Peter Vangheluwe
[DESCRIPTION]
This protocol describes the seeding, fixation and staining of samples for immunofluorescent visualization of ATP13A2 and CD63.
[STEPS]
1. Seed cells: 75 000 cells/well (SH-SY5Y) in a 12-well plate with coverslips... | ["Seed cells: 75 000 cells/well (SH-SY5Y) in a 12-well plate with coverslips. Allow the cells to attach and grow for 2880 min.", "Wash the cells with ice-cold PBS.", "Wash the cells twice with ice-cold PBS.", "Permeabilization and blocking with a mixture of 5% BSA (Roth) and 0.5% saponin (Sigma) (diluted in PBS) (refer... |
70,128 | DNA extraction from fecal samples | 4 | dx.doi.org/10.17504/protocols.io.5jyl8jnorg2w/v1 | https://www.protocols.io/view/dna-extraction-from-fecal-samples-cgqqtvvw | Anique Ahmad, Arya Gautam, Tsedenia Denekew, Aashish Jha | TITLE: DNA extraction from fecal samples
AUTHORS: Anique Ahmad, Arya Gautam, Tsedenia Denekew, Aashish Jha
[DESCRIPTION]
DNA Extraction from fecal samples
[BEFORE_START]
Label the following:
ZR BashingBeadTM Lysis Tubes (0.1 & 0.5 mm)
ZymoSpinTM III-F Filter in Collection Tube
Collection Tube
ZymoSpin... | ["Transfer fecal sample to ZR BashingBead™ Lysis Tube (0.1 & 0.5 mm) and add ZymoBIOMICS™ Lysis Solution:", "Flash frozen fecal samples will be solid and an aliquot (15 mg) of feces is expected in a 2mL container (Table 1). Add 250 µL of ZymoBIOMICS™ Lysis Solution to the fecal sample and homogenize evenly using the ho... |
57,315 | The effects of cognitive training in healthy community residing Thai elderly: randomized controlled trial | 1 | null | https://www.protocols.io/view/the-effects-of-cognitive-training-in-healthy-commu-b38bqrsn | Muthita Phanasathit, Chaichana Nimnuan, Vitool Lohsoonthorn | TITLE: The effects of cognitive training in healthy community residing Thai elderly: randomized controlled trial
AUTHORS: Muthita Phanasathit, Chaichana Nimnuan, Vitool Lohsoonthorn
[DESCRIPTION]
Aim: Cognitive training intervention (CTI) in the elderly is associated with a risk reduction of dementia; however, the ... | ["[Study design] - 1:1 ratio 2-arm parallel single-blinded intervention randomized controlled trial study design (RCT) with a single-blinded assessor. \n- All cognitive function outcomes were assessed by trained blinded psychologists not involved in the recruitment process and experimental phase.\n- Study Endpoint Clas... |
98,025 | "Reward perseveration is shaped by GABAA-mediated dopamine pauses", Burwell et al | 0 | dx.doi.org/10.17504/protocols.io.j8nlk8ekdl5r/v1 | https://www.protocols.io/view/34-reward-perseveration-is-shaped-by-gabaa-mediat-dbyh2pt6 | Sasha Burwell, HaiDun, MICHAEL R TADROSS | TITLE: "Reward perseveration is shaped by GABAA-mediated dopamine pauses", Burwell et al
AUTHORS: Sasha Burwell, HaiDun, MICHAEL R TADROSS
[DESCRIPTION]
This collection of protocols details the experiments and analysis performed for the Burwell et al paper "Reward perseveration is shaped by GABAA-mediated dopa... | [] |
73,705 | TABLE-seq for strand-specific RNA sequencing | 4 | dx.doi.org/10.17504/protocols.io.8epv5jrw6l1b/v1 | https://www.protocols.io/view/table-seq-for-strand-specific-rna-sequencing-cj8hurt6 | Yanjun zhang, Ying Tang, Dong Fang | TITLE: TABLE-seq for strand-specific RNA sequencing
AUTHORS: Yanjun zhang, Ying Tang, Dong Fang
[DESCRIPTION]
This protocol utilizes the Tn5, a widely used transposase, to perform single-strand DNA sequencing. Tn5 can tagment single-strand DNA and ligate transposon cargo to the 3’ end. We developed a tagmentation-base... | ["RNA extractionRNA extraction is performed by RNeasy Plus Mini Kit (Qiagen, Cat. #74134). Or any conventional method. \n\n1.1 Harvest and wash cells with PBS once. \n1.2 Lyse the cell with 350 μl Buffer RLT and vortex for 30 s. \n1.3 Add the lysates to a gDNA Eliminator spin column and centrifuge at 10,000 rpm for... |
41,874 | FloodLAMP Binding Solution Prep v1.1 | 1 | dx.doi.org/10.17504/protocols.io.bk5sky6e | https://www.protocols.io/view/floodlamp-binding-solution-prep-v1-1-bk5sky6e | Randy True | TITLE: FloodLAMP Binding Solution Prep v1.1
AUTHORS: Randy True
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The Binding Solution includes NaI, HCl, Triton-X100, and water. We have had lots of trouble with it, largely due to a mistake that has been corrected. In our hands currently, the Binding S... | ["Weight out 45g of NaI into 50mL Falcon Tube", "Add 1st traunch of water to 45ml", "Vortex, shake and then vortex again until fully mixed", "Add 2nd traunch of water to 46mL", "Vortex, shake and then vortex again until fully mixed", "Vacuum filter (or wait and vacuum filter many tubes at the end)", "Add .5mL of 1N HCl... |
75,593 | Modified Organic Extraction Protocol (Pedersen et al., 2016) | 4 | dx.doi.org/10.17504/protocols.io.ewov1o3oklr2/v1 | https://www.protocols.io/view/modified-organic-extraction-protocol-pedersen-et-a-cm3hu8j6 | Mikkel Pedersen | TITLE: Modified Organic Extraction Protocol (Pedersen et al., 2016)
AUTHORS: Mikkel Pedersen
[DESCRIPTION]
A modified version of the organic extraction protocol used in Wales et al., 2014.
Protocol successful at reconstructing the biodiversity of 15 kya sediment core, including a few fish species
[BEFORE_START]
Rev... | ["[Sample preparation & cell lysis] ADD 2 g of sediment sample to a sterile spin tube\n\nADD 170 µg of proteinase K to the sample\n\nADD 3 mL of lysis buffer to the sample\n\nVORTEX sample at max speed for 40 s", "[Sample preparation & cell lysis] ADD an additional 170 µg of proteinase K to each sample\n\nINCUB... |
107,774 | Electron Microscopy of Brain Tissue Samples | 0 | dx.doi.org/10.17504/protocols.io.rm7vzjd82lx1/v1 | https://www.protocols.io/view/electron-microscopy-of-brain-tissue-samples-dmg643ze | Livia Hecke Morais, Mark Ladinski | TITLE: Electron Microscopy of Brain Tissue Samples
AUTHORS: Livia Hecke Morais, Mark Ladinski
[DESCRIPTION]
Protocol has been approved by the California Institute of Technology’s Institutional Animal Care
and Use Committee (IACUC).
[STEPS]
SECTION: Brain perfusion
1. Mice were anesthetized with 150 uL pentobarbital (... | ["[Brain perfusion] Mice were anesthetized with 150 uL pentobarbital (Euthasol), and their hearts were punctured.", "[Brain perfusion] Mice were perfused with 50 mL of 37°C PBS followed by 50 mL of 37°C 4% paraformaldehyde (PFA) at a flow rate of 6 mL/min.", "[Brain perfusion] Brains were dissected and immediately plac... |
84,608 | Modified Frame-projected Independent Fiber Photometry (FIP) System_Triggering system | 4 | dx.doi.org/10.17504/protocols.io.kxygx3e6wg8j/v1 | https://www.protocols.io/view/modified-frame-projected-independent-fiber-photome-cwu8xezw | Kenta M. Hagihara | TITLE: Modified Frame-projected Independent Fiber Photometry (FIP) System_Triggering system
AUTHORS: Kenta M. Hagihara
[DESCRIPTION]
Frame-projected independent fiber photometry (FIP) is a method to measure fluorescent sensor signals through optical fibers implanted in living animals, using a camera to record video of... | ["[Setting up an experimental PC and Teensy 4.1 device] Connect Teensy 4.1 device to the experimental PC using a USB cable, set proper COM port in the Arduino app, and upload the .ino sketch to the device. How to find and set up the corresponding COM port can be found here: https://support.arduino.cc/hc/en-us/articles/... |
21,623 | Post-retraction citation: a case for radiology-imaging diagnostic | 1 | dx.doi.org/10.17504/protocols.io.zcxf2xn | https://www.protocols.io/view/post-retraction-citation-a-case-for-radiology-imag-zcxf2xn | Sorana D. Bolboacă, Diana-Victoria Buhai, Maria Aluaș, Adriana E. Bulboacă | TITLE: Post-retraction citation: a case for radiology-imaging diagnostic
AUTHORS: Sorana D. Bolboacă, Diana-Victoria Buhai, Maria Aluaș, Adriana E. Bulboacă
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Citation of a manuscript could be seen as a measure of study visibility and usefulness. Citatio... | ["[Availability and Eligibility]\nDefining de search strategyKeywords: ((diagnostic or diagnosis) and (imaging or radiology)) AND ((Retracted Publication[sb] OR Retraction of Publication[sb])) Source: PubMed Clinical Queries (https://www.ncbi.nlm.nih.gov/pubmed/clinical)Restrictions: Clinical Study Categories- Categor... |
60,064 | Overview of scRNA-seq of Human Knee Articular Cartilage | 4 | dx.doi.org/10.17504/protocols.io.5qpvob93dl4o/v1 | https://www.protocols.io/view/overview-of-scrna-seq-of-human-knee-articular-cart-b6v8re9w | molmer , Martin Lotz | TITLE: Overview of scRNA-seq of Human Knee Articular Cartilage
AUTHORS: molmer , Martin Lotz
[DESCRIPTION]
The overview provides sub-protocols for each step required to complete scRNA-seq from human knee articular cartilage.
[STEPS]
1. Tissue Acquisition
dx.doi.org/10.17504/protocols.io.14egn7996v5d/v1
2. Tissue Q... | ["Tissue Acquisition\ndx.doi.org/10.17504/protocols.io.14egn7996v5d/v1", "Tissue Quality Control\ndx.doi.org/10.17504/protocols.io.n2bvj695nlk5/v1", "Single-Cell Isolation\ndx.doi.org/10.17504/protocols.io.14egn765qv5d/v1", "cDNA Library Preparation\ndx.doi.org/10.17504/protocols.io.bp2l6175rvqe/v1", "Data Processing a... |
99,987 | Labeling and DAB oxidation of EdU-treated HEK293T cells with Cy5 azide and Fe-TAML azide for light and transmission electron microscopy | 0 | dx.doi.org/10.17504/protocols.io.n2bvjn8jxgk5/v1 | https://www.protocols.io/view/labeling-and-dab-oxidation-of-edu-treated-hek293t-ddvt266n | Stephen Adams, Mason Mackey, Mark H. Ellisman | TITLE: Labeling and DAB oxidation of EdU-treated HEK293T cells with Cy5 azide and Fe-TAML azide for light and transmission electron microscopy
AUTHORS: Stephen Adams, Mason Mackey, Mark H. Ellisman
[DESCRIPTION]
This protocol outlines the click chemistry labeling of EdU-pulsed DNA with Fe-TAML azide to catalyze DAB ox... | ["HEK293T cells were plated onto MatTek dishes containing 35mm glass bottom No. 0 coverslips coated with poly-d-lysine.", "The next day, 10 μM EdU is added to the cells and incubated for 720 min", "Cells are fixed with 2% glutaraldehyde (16220, Electron Microscopy Sciences) in 0.1 M sodium cacodylate buffer (18851, Ted... |
35,635 | Systematic review and meta-analysis protocol examining the effect of vitamin D status and supplementation on urinary tract infection | null | dx.doi.org/10.17504/protocols.io.be2tjgen | null | Niwanda Yogiswara, Yusuf Azmi, Farapti farapti, Yufi Aulia Azmi | TITLE: Systematic review and meta-analysis protocol examining the effect of vitamin D status and supplementation on urinary tract infection
AUTHORS: Niwanda Yogiswara, Yusuf Azmi, Farapti farapti, Yufi Aulia Azmi
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-al... | ["Review question: The present systematic review aims to investigate whether 25(OH)D levels differ among UTI patients and healthy participants, investigate the association between vitamin D status and UTI, and investigate the role of vitamin D supplementation to reduce UTI.Population: General population without age, g... |
null | null | null | dx.doi.org/10.17504/protocols.io.matc2en | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>A protocol for preparing phage lysate of Brucella organisms employing a lytic brucellaphage is given here.</p>
[STEPS]
?. | [] |
33,388 | A modified protocol for rapid HMW DNA isolation from plant tissues using CTAB | null | dx.doi.org/10.17504/protocols.io.bcukiwuw | null | Miguel Flores | TITLE: A modified protocol for rapid HMW DNA isolation from plant tissues using CTAB
AUTHORS: Miguel Flores
[STEPS]
?. Collect the tissue sample in a 50 mL Falcon tube and snap freeze in liquid nitrogen.
?. Pour a small amount of liquid nitrogen into a mortar that is precooled to −70 °C. Place the frozen sample into t... | ["Collect the tissue sample in a 50 mL Falcon tube and snap freeze in liquid nitrogen.", "Pour a small amount of liquid nitrogen into a mortar that is precooled to −70 °C. Place the frozen sample into the mortar containing the liquid nitrogen.", "Start slowly and increase the intensity of grinding as the liquid nitroge... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.