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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null | null | null | dx.doi.org/10.17504/protocols.io.chmt45 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is the protocol for the Q5® Site-Directed Mutagenesis Kit without competent cells
[STEPS]
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31,074 | Chloral Hydrate Seed Clearing | null | dx.doi.org/10.17504/protocols.io.bakaicse | null | Gabrielle Sandstedt, Andrea Sweigart | TITLE: Chloral Hydrate Seed Clearing
AUTHORS: Gabrielle Sandstedt, Andrea Sweigart
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">To characterize early seed development in Mimulus (1-5 days after pollination), we clear seeds with chloral hydrate and quickly obtain images of embryo and endosperm dev... | ["[Dissecting fruit and clearing]\nEmasculate a bud from some maternal plant. 2 to 3 days later pollinate by selfing/outcrossing or use an unfertilized fruit.", "[Dissecting fruit and clearing]\nRemove the developing fruit 1 to 5 days after pollination or 2 to 3 days after emasculation. In Mimulus, this protocol is use... |
58,684 | Detailed Western Blotting (Immunoblotting) Protocol | 4 | dx.doi.org/10.17504/protocols.io.b5i4q4gw | https://www.protocols.io/view/detailed-western-blotting-immunoblotting-protocol-b5i4q4gw | Rasheed Sule, Gabriela Rivera, Aldrin V Gomes | TITLE: Detailed Western Blotting (Immunoblotting) Protocol
AUTHORS: Rasheed Sule, Gabriela Rivera, Aldrin V Gomes
[DESCRIPTION]
Western Blotting, which is probably better referred to as immunoblotting, is one of the most commonly used biological methods worldwide. This technique is capable of detecting an indivi... | ["[Sample preparation] Sample preparation can be simple or complex, depending on the source of the sample and the location of the target protein. It is recommended that you consult a dedicated article with procedures for optimal sample preparation.\nThis protocol assumes you have already prepared your sample and are re... |
67,448 | Via Keto Apple Gummies Australia Reviews- Price or Chemist Warehouse Buy | 1 | dx.doi.org/10.17504/protocols.io.bp2l61qndvqe/v1 | https://www.protocols.io/view/via-keto-apple-gummies-australia-reviews-price-or-cd4ys8xw | health | TITLE: Via Keto Apple Gummies Australia Reviews- Price or Chemist Warehouse Buy
AUTHORS: health
[DESCRIPTION]
Via Keto Apple Gummies - Natural products are always a better choice due to their medicinal potential and guaranteed safety.
[STEPS]
1. Via Keto Apple Gummies is a weight loss component primarily based on a... | ["Via Keto Apple Gummies is a weight loss component primarily based on a ketogenic food regimen that includes essential nutrients together with omega-3s, multivitamins, as well as protein to offer speedy weight management effects without facet effects. Official Web: https://www.mynewsdesk.com/nealthnewscart/pressreleas... |
35,720 | SNARE-seq2 | 1 | dx.doi.org/10.17504/protocols.io.be5gjg3w | https://www.protocols.io/view/snare-seq2-be5gjg3w | Nongluk Plongthongkum, Dinh H Diep, Song Chen, Blue Lake, Kun Zhang | TITLE: SNARE-seq2
AUTHORS: Nongluk Plongthongkum, Dinh H Diep, Song Chen, Blue Lake, Kun Zhang
[DESCRIPTION]
To study the heterogeneity of complex tissues by joint profiling of gene expression and its regulation, we require an accurate and high-throughput method. Here we described improved high-throughput combinato... | ["[Reagent setup] 40% (wt/vol) PEG 6000. Weigh 16.0 g of PEG 6000 in 50 mL tube. Add nuclease-free water and bring the total volume to 40 mL. Rotate the tube at room temperature until PEG 6000 completely dissolved. Spin down the tube at 200 g for 2 min, at room temperature to remove the tiny bubble. CRITICAL: 40% (wt/v... |
27,390 | Tissue Procurement: Biosafety Guidelines | 1 | dx.doi.org/10.17504/protocols.io.6y6hfze | https://www.protocols.io/view/tissue-procurement-biosafety-guidelines-6y6hfze | Kerry Wiles | TITLE: Tissue Procurement: Biosafety Guidelines
AUTHORS: Kerry Wiles
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The biosafety guidelines in this protocol are based on the Center for Disease Control's </span><span style = "font-style:italic;">Biosafety in Microbiology and Biomedical Labora... | ["[Tissue Procurement: Biosafety Guidelines]\nCollection is done by trained personnel and all products are handled separately and under as sterile conditions as possible. You will always take the necessary precautions for your safety, BUT also take the necessary precautions to protect the tissue FROM you.", "[Tissue Pr... |
41,996 | CollectingCitationsfromText | 5 | dx.doi.org/10.17504/protocols.io.bk9kkz4w | https://www.protocols.io/view/collectingcitationsfromtext-bk9kkz4w | Rebecca Hedreen | TITLE: CollectingCitationsfromText
AUTHORS: Rebecca Hedreen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Basic steps and scripts used for translating text citations to bibtex files suitable for loading into citation management software or citation analysis scripts. 3 publically available webpage ... | ["[Preparing text file]\nCopy citations from the source document(s) into a text (.txt) document.", "[Preparing text file]\nEdit the text document so that each citation is on a separate line with one blank line between each citation. Not all the scripts require a blank line between citations, but it does improve readabi... |
10,256 | 1% Agarose Gel Electrophoresis Prep | null | dx.doi.org/10.17504/protocols.io.m9qc95w | null | Claire Rycroft, Ben JG. Sutherland | TITLE: 1% Agarose Gel Electrophoresis Prep
AUTHORS: Claire Rycroft, Ben JG. Sutherland
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Ararose (1%) gel electrophoresis for genomic DNA quality checking.</div><div class = "text-block">This protocol comes with no guarantees from the authors.</div></div... | ["[Gel Prep]\nWeigh out 2.5g of powdered agarose.", "[Gel Prep]\nAdd 250mL of 1XTAE buffer to a 1.0L Erlenmeyer flask.Note:Be mindful to use best practices when making solutions. Make sure the glassware you are using has been properly cleaned and has been pre-rinsed with whatever solution you will be working with, in t... |
null | null | null | dx.doi.org/10.17504/protocols.io.magc2bw | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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70,154 | fastANI analysis protocol | 5 | null | https://www.protocols.io/view/fastani-analysis-protocol-cgritv4e | Jamie Harrison, David J Studholme | TITLE: fastANI analysis protocol
AUTHORS: Jamie Harrison, David J Studholme
[DESCRIPTION]
this is the protocol to conduct ani analysis between groups of genomes using fastANI and produce the heatmap figure in R using the pheatmap package
[STEPS]
SECTION: create directories
1.2. mkdir analysis query_genomes reference_... | ["[create directories] mkdir analysis query_genomes reference_genomes", "[create directories] move to query dir", "[create directories]", "[create directories]", "[create directories]", "Create directory structure and link files", "[create directories] move to reference dir", "[create directories]", "[create directorie... |
22,753 | Microbiological contamination of young children’s hands in rural Bangladesh: Associations with child age and observed hand cleanliness as proxy | null | dx.doi.org/10.17504/protocols.io.2f9gbr6 | null | Sarker Masud Parvez, Rashidul Azad, Amy J. Pickering, Laura H Kwong, Benjamin F. Arnold, Musarrat Jabeen Rahman, Md. Zahidur Rahman, Mahfuja Alam, Debashis Sen, Sharmin Islam, Mahbubur Rahman, John M. Colford, Jr, Stephen P. Luby, Leanne Unicomb, Ayse Ercumen | TITLE: Microbiological contamination of young children’s hands in rural Bangladesh: Associations with child age and observed hand cleanliness as proxy
AUTHORS: Sarker Masud Parvez, Rashidul Azad, Amy J. Pickering, Laura H Kwong, Benjamin F. Arnold, Musarrat Jabeen Rahman, Md. Zahidur Rahman, Mahfuja Alam, Debashis Sen,... | [] |
44,408 | Fluorescence Recovery after Photobleaching (FRAP) in adult C. elegans nuclei | 4 | dx.doi.org/10.17504/protocols.io.bpkymkxw | https://www.protocols.io/view/fluorescence-recovery-after-photobleaching-frap-in-bpkymkxw | Laura Breimann, Kustrim Cerimi, Vic-Fabienne Schumann, Stephan Preibisch, Sevinc Ercan, Andrew Woehler | TITLE: Fluorescence Recovery after Photobleaching (FRAP) in adult C. elegans nuclei
AUTHORS: Laura Breimann, Kustrim Cerimi, Vic-Fabienne Schumann, Stephan Preibisch, Sevinc Ercan, Andrew Woehler
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Protocol for Fluorescence Recovery after Photoble... | ["[Preparation of agarose pads]\nPrepare two glass slides as spacers by taping one layer of lab tape along the slides' long side. Tape them to the table, separated to leave space for one glass slide in between them.", "[Preparation of agarose pads]\nDissolve agarose in M9 to create solution and slowly melt in microwav... |
74,741 | Recombinant expression and purification of HIV-1 RT | 4 | dx.doi.org/10.17504/protocols.io.3byl4jzyjlo5/v1 | https://www.protocols.io/view/recombinant-expression-and-purification-of-hiv-1-r-ck8vuzw6 | Javiera A Avilés, Tamara Matute, Isaac Núñez, Maira Rivera, Javiera Reyes, Jenny Molloy, Cesar A Ramirez-Sarmiento, Fernan Federici | TITLE: Recombinant expression and purification of HIV-1 RT
AUTHORS: Javiera A Avilés, Tamara Matute, Isaac Núñez, Maira Rivera, Javiera Reyes, Jenny Molloy, Cesar A Ramirez-Sarmiento, Fernan Federici
[DESCRIPTION]
This protocol has been optimized for the recombinant expression of HIV-1 RT. The sequence of the plasmid... | ["[DAY 1 – Plasmid transformation] Transform 100 ng of plasmid containing HIV-1 RT into E. coli BL21(DE3) competent cells using either heat shock or electroporation.", "[DAY 1 – Plasmid transformation] Spread transformed cells in LB Agar plates supplemented with 0.05 mg/mL Kan. Grow plate overnight at 37 °C.", "[DAY 2 ... |
68,477 | Modified Qiagen DNeasy Blood and Tissue extraction method (Cat. No. / ID: 69506) for eDNA extraction from filters (Nitrocellulose Mixed Ester membrane filters or similar) | 4 | dx.doi.org/10.17504/protocols.io.8epv59y4jg1b/v1 | https://www.protocols.io/view/modified-qiagen-dneasy-blood-and-tissue-extraction-ce45tgy6 | Yoamel Milián-García | TITLE: Modified Qiagen DNeasy Blood and Tissue extraction method (Cat. No. / ID: 69506) for eDNA extraction from filters (Nitrocellulose Mixed Ester membrane filters or similar)
AUTHORS: Yoamel Milián-García
[DESCRIPTION]
The commercial Qiagen DNeasy Blood and Tissue kit constitutes one of the most used kits in Molecu... | ["Allow a filter to thaw on a sterile Petri Dish (e.g., Fisher Scientific Catalog No. FB0875713 or FB0875713A) and cut into quarters (halves can be used to decrease the number of extractions per filter). Cut the filter quarters (or halves) into strips using sterile razor blades. Filter strip manipulations at this step ... |
null | null | null | dx.doi.org/10.17504/protocols.io.qywdxxe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Protocol for collecting gas for measurement of carbon isotope descrimination during photosynthesis.</p>
<p> </p>
<p>See the following references for more background:</p>
<p>H. Griffiths (1993) <a href="https://link.springer.com/book/10.1007/978-94-011-1566-7" target="_blank" ... | [] |
30,987 | CIDC_S16_LC_MS_Celegans_Extraction_Protocol | 1 | dx.doi.org/10.17504/protocols.io.bahjib4n | https://www.protocols.io/view/cidc-s16-lc-ms-celegans-extraction-protocol-bahjib4n | Brianna M Garcia, Carter Asef | TITLE: CIDC_S16_LC_MS_Celegans_Extraction_Protocol
AUTHORS: Brianna M Garcia, Carter Asef
[DESCRIPTION]
A sample preparation protocol for lyophlized C. elegans samples to be analyzed via LC-MSMS
[STEPS]
SECTION: Homogenization
1. Samples are removed from -80 °C
SECTION: Homogenization
2. (3) 2.0mm zirconium oxide b... | ["[Homogenization] Samples are removed from -80 °C", "[Homogenization] (3) 2.0mm zirconium oxide beads and ~ 75 µL volume of 0.5mm glass beads are added to each sample tube.", "[Homogenization] Samples are placed in Tissuelyser II using adapter trays chilled at -80C and homogenized at 1800rpm for 3 min.", "[Homogeniz... |
36,237 | Footprint-Free Genome Editing of iPSC Using Alt-R CRISPR/Cas9 | null | dx.doi.org/10.17504/protocols.io.bfmmjk46 | https://www.protocols.io/view/footprint-free-genome-editing-of-ipsc-using-alt-r-bfmmjk46 | Jacob Marsh, Rj Martinez, Celeste Karch | TITLE: Footprint-Free Genome Editing of iPSC Using Alt-R CRISPR/Cas9
AUTHORS: Jacob Marsh, Rj Martinez, Celeste Karch
[STEPS]
?. [Preparing iPSCs for Nucleofection]
Coat 1 well of a 6-well plate with of Matrigel for at
1 ml
37 °C
?. [Preparing iPSCs for Nucleofection]
Add of DMEM/F12 to a 15ml conical tue
5 ml
?.... | ["[Preparing iPSCs for Nucleofection]\nCoat 1 well of a 6-well plate with of Matrigel for at\n1 ml\n37 °C", "[Preparing iPSCs for Nucleofection]\nAdd of DMEM/F12 to a 15ml conical tue\n5 ml", "[Preparing iPSCs for Nucleofection]\nThaw vial of cells in water bath for approximately\n37 °C", "[Preparing iPSCs for Nu... |
55,922 | My demo protocol | 1 | null | https://www.protocols.io/view/my-demo-protocol-b2usqewe | Gerard Weatherby | TITLE: My demo protocol
AUTHORS: Gerard Weatherby
[DESCRIPTION]
API test
[STEPS]
SECTION: Section 1
1. Do something.
SECTION: Section 1
1.1. Start here
SECTION: Section 1
1.2. | ["[Section 1] Do something.", "[Section 1] Start here", "[Section 1]"] |
35,596 | Artificial Cerebrospinal Fluid I (ACSF.I) | null | dx.doi.org/10.17504/protocols.io.bezkjf4w | null | Allen Institute for Brain Science | TITLE: Artificial Cerebrospinal Fluid I (ACSF.I)
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used to prepare Artificial Cerebrospinal Fluid I (ACSF.I). ACSF.I is used for applications including transcardial perfusion prior to fresh mous... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.gusbwwe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<div class="page" title="Page 2">
<div class="layoutArea">
<div class="column">
<p>Western blot detection of proteins requires separation of protein mixtures by electrophoresis, followed by transfer of the separated proteins to nitrocellulose or PVDF membranes for detection.The ... | [] |
46,008 | Human Tissue Slicing and Dissections for Nuclear Isolations | 1 | dx.doi.org/10.17504/protocols.io.bq6ymzfw | https://www.protocols.io/view/human-tissue-slicing-and-dissections-for-nuclear-i-bq6ymzfw | Allen Institute for Brain Science | TITLE: Human Tissue Slicing and Dissections for Nuclear Isolations
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the slicing and microdissection procedure on frozen post-mortem human brain tissue to be used to isolate nuclei for su... | [] |
93,199 | Stereotaxic viral injections and array implantation | 1 | dx.doi.org/10.17504/protocols.io.14egn31q6l5d/v1 | https://www.protocols.io/view/stereotaxic-viral-injections-and-array-implantatio-c69pzh5n | Mai-Anh Vu, mwhowe | TITLE: Stereotaxic viral injections and array implantation
AUTHORS: Mai-Anh Vu, mwhowe
[DESCRIPTION]
We have developed a new micro-fiber array approach capable of chronically measuring and optogenetically manipulating local dynamics across over 100 targeted locations simultaneously in head-fixed and freely moving mice... | ["[viral injection] Mice were anesthetized under isoflurane (1-3%) and placed in a stereotaxic frame.", "[viral injection] Mice were injected with AAVs to express genetically encoded proteins for optical measurements and manipulations. Virus (~200-800nL per site) was injected stereotaxically through a pulled glass pipe... |
75,970 | PCR-NGS for RNA viruses | 4 | dx.doi.org/10.17504/protocols.io.x54v9d361g3e/v1 | https://www.protocols.io/view/pcr-ngs-for-rna-viruses-cnfavbie | Masayasu Misu, Tomoki Yoshikawa, Satoko Sugimoto, Yuki Takamatsu, Takeshi Kurosu, Yukiteru Ouji, Masahide Yoshikawa, Masayuki Shimojima, Hideki Ebihara, Masayuki Saijo | TITLE: PCR-NGS for RNA viruses
AUTHORS: Masayasu Misu, Tomoki Yoshikawa, Satoko Sugimoto, Yuki Takamatsu, Takeshi Kurosu, Yukiteru Ouji, Masahide Yoshikawa, Masayuki Shimojima, Hideki Ebihara, Masayuki Saijo
[DESCRIPTION]
This PCR-NGS were optimized for an NGS machine, MinION. These methods do not require nucleic acid... | ["[Preparation for virus supernatant] Centrifuge the working stock virus to remove debris.\n 6000 x g, 10 min", "[Preparation for virus supernatant] Unwanted DNA and RNA mainly originating from the virus-infected cells are digested using .", "[The viral RNA extraction] The viral genomic RNA extraction is performed usin... |
100,136 | Single-cell single-unit recordings in vitro | 0 | dx.doi.org/10.17504/protocols.io.yxmvme269g3p/v1 | https://www.protocols.io/view/single-cell-single-unit-recordings-in-vitro-dd2g28bw | Nicola Biagio Mercuri | TITLE: Single-cell single-unit recordings in vitro
AUTHORS: Nicola Biagio Mercuri
[DESCRIPTION]
Single units in slices
[STEPS]
SECTION: Single-cell single-unit recordings
1. The slice is placed in a submerged recording chamber in continuously flowing ACSF (34°C) saturated with O2/CO2 gas mixture (95/5%).
SECTION: Sin... | ["[Single-cell single-unit recordings] The slice is placed in a submerged recording chamber in continuously flowing ACSF (34°C) saturated with O2/CO2 gas mixture (95/5%).", "[Single-cell single-unit recordings] ACSF composition (in mM): 126 NaCl, 2.5 KCl,1.2 MgCl2, 1.2 NaH2PO4, 2.4 CaCl2, 10 glucose and 25 NaHCO3.", "[... |
null | null | null | dx.doi.org/10.17504/protocols.io.hjsb4ne | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
A protocol to separate chloroplasts from diatom cells using ammonium fluoride to permeate the silica frustrule and a percoll gradient to separate the plastid from other cellular components.
[BEFORE_START]
Make sure all buffers are prepared according to the instructions in "Buff... | [] |
18,288 | SYSB 3036 W11: Gene Expression and RNA-Seq | null | dx.doi.org/10.17504/protocols.io.v4qe8vw | null | Frank Aylward | TITLE: SYSB 3036 W11: Gene Expression and RNA-Seq
AUTHORS: Frank Aylward
[STEPS]
?. [Getting started]
Last tutorial we went over basic read mapping protocols using bowtie and SAMtools. We used data from a infection experiment that used Mycobacterium smegmatis and a bacteriophage called D29. We examined only one time-p... | ["[Getting started]\nLast tutorial we went over basic read mapping protocols using bowtie and SAMtools. We used data from a infection experiment that used Mycobacterium smegmatis and a bacteriophage called D29. We examined only one time-point that took place 15 minutes after infection. Today we will finish analyzing th... |
null | null | null | dx.doi.org/10.17504/protocols.io.gzebx3e | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>Gibson assembly using NEBuilder HiFi DNA assembly kit. Specification of the original NEB protocol.</p>
[STEPS]
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98,973 | Brain Data Alchemy Project: Meta-Analysis of Re-Analyzed Public Transcriptional Profiling Data in the Gemma Database | 0 | dx.doi.org/10.17504/protocols.io.j8nlk84jxl5r/v1 | https://www.protocols.io/view/brain-data-alchemy-project-meta-analysis-of-re-ana-dcv52w86 | Megan Hagenauer, Cosette Rhoads, Jinglin Xiong, Duy Manh Nguyen, Erin Hernandez, Annaka Saffron, Amrita Kondur, Elizabeth Flandreau | TITLE: Brain Data Alchemy Project: Meta-Analysis of Re-Analyzed Public Transcriptional Profiling Data in the Gemma Database
AUTHORS: Megan Hagenauer, Cosette Rhoads, Jinglin Xiong, Duy Manh Nguyen, Erin Hernandez, Annaka Saffron, Amrita Kondur, Elizabeth Flandreau
[DESCRIPTION]
Over the past two decades, transcription... | ["[Project Preparation: Environment Set-Up] Install R and RStudio", "[Project Preparation: Environment Set-Up] Install R", "[Project Preparation: Environment Set-Up] Install R Studio", "[Project Preparation: Environment Set-Up] Follow the Brain Data Alchemy code repository on Github", "[Project Preparation: Environment... |
94,402 | Chemogenetic modulation of catecholaminergic neurons | 1 | dx.doi.org/10.17504/protocols.io.rm7vzxdz5gx1/v1 | https://www.protocols.io/view/chemogenetic-modulation-of-catecholaminergic-neuro-c8faztie | Cristian González-Cabrera, Csilla Novák, Maria P. Contreras, Ernesto Durán, Matthias Prigge | TITLE: Chemogenetic modulation of catecholaminergic neurons
AUTHORS: Cristian González-Cabrera, Csilla Novák, Maria P. Contreras, Ernesto Durán, Matthias Prigge
[DESCRIPTION]
This protocol outlines a method for modulating noradrenergic and dopaminergic neuronal activity in the LC and SNc-VTA, respectively, using Cre-d... | ["[Stereotactic injection] Stereotactic injection of viruses into DbH-Cre (JAX# 033953) or DAT-Cre (JAX# 006660) animals\n\nViral Construct:\npAAV-hSyn-DIO-hM4D(Gi)-mCherry (Addgene link) \nVolume: 400ul\npAAV-hSyn-DIO-hM3D(Gq)-mCherry (Addgene link)\nVolume: 400ul\n\n(in our experiment we mix our DIO-hTyr Virus 1:1 w... |
null | null | null | dx.doi.org/10.17504/protocols.io.kb6csre | null | null | TITLE: No Title
AUTHORS:
[STEPS]
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52,924 | MicroCT protocols for scanning of embryos and juvenile Hexaplex trunculus | 4 | dx.doi.org/10.17504/protocols.io.bxw4ppgw | https://www.protocols.io/view/microct-protocols-for-scanning-of-embryos-and-juve-bxw4ppgw | Eva Chatzinikolaou, Kleoniki Keklikoglou | TITLE: MicroCT protocols for scanning of embryos and juvenile Hexaplex trunculus
AUTHORS: Eva Chatzinikolaou, Kleoniki Keklikoglou
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Micro-computed tomography (micro-CT) is a high-resolution 3D-imaging technique which is now increasingly applied i... | ["[Sample preparation]\nAnesthetization of embryos and juvenile gastropods with 7% MgCl2.", "[Sample preparation]\nSample placement inside a plastic white pipette tip without any scanning medium (in the air).", "[microCT scanning]", "[microCT scanning]\nScanning parameters for embryos and juvenile Hexaplex trunculusVol... |
25,105 | IVF Bioscience Bovine Slaughterhouse Protocol | null | dx.doi.org/10.17504/protocols.io.4rrgv56 | null | Jake Silcock | TITLE: IVF Bioscience Bovine Slaughterhouse Protocol
AUTHORS: Jake Silcock
[STEPS]
?. [Aspiration and IVM]
Dish and Media Preparation
?. [Aspiration and IVM]
Add of BO-IVM medium per well to 4-well plates without an Oil overlay and place in the incubator
500 µl
?. [Aspiration and IVM]
Additionally, prepare one 35 mil... | ["[Aspiration and IVM]\nDish and Media Preparation", "[Aspiration and IVM]\nAdd of BO-IVM medium per well to 4-well plates without an Oil overlay and place in the incubator\n500 µl", "[Aspiration and IVM]\nAdditionally, prepare one 35 millimetre dish with of BO-IVM per 4-well plate and place in the incubator without ... |
89,942 | Vesicle Fusion on SiO2 Substrates | 1 | null | https://www.protocols.io/view/vesicle-fusion-on-sio2-substrates-c33wyqpe | Paul Stevenson, Nicole Voce | TITLE: Vesicle Fusion on SiO2 Substrates
AUTHORS: Paul Stevenson, Nicole Voce
[DESCRIPTION]
This protocol outlines the steps to produce large area, uniform supported lipid bilayers on SiO2 substrates with or without patterned features.
[STEPS]
SECTION: Substrate cleaning
1. Clean plain SiO2 or TiO2-patterned substrat... | ["[Substrate cleaning] Clean plain SiO2 or TiO2-patterned substrates by sonicating them in a 1:1 IPA:Acetone mixture for ~2 minutes\nDry with a steady stream of N2", "[Substrate cleaning] Oxygen plasma clean the substrates for 2 minutes to remove any residual surface contamination", "[Vesicle prep] Prepare a 1.2 mg/mL ... |
78,250 | CellProfiler Pipeline to Obtain Pearson's correlation coefficients for TMEM55B or pRab10 and RILPL1 | 5 | dx.doi.org/10.17504/protocols.io.rm7vzbqp5vx1/v1 | https://www.protocols.io/view/cellprofiler-pipeline-to-obtain-pearson-39-s-corre-cqnivvce | Chloe A Hecht, Suzanne Pfeffer | TITLE: CellProfiler Pipeline to Obtain Pearson's correlation coefficients for TMEM55B or pRab10 and RILPL1
AUTHORS: Chloe A Hecht, Suzanne Pfeffer
[DESCRIPTION]
We present here a CellProfiler software pipeline to quantify the intensity of endogenous TMEM55B or pRab10 in LRRK2 R1441C or VPS35 D620N MEF cells transf... | ["[Expansion Microscopy TMEM55B and Myc-RILPL1 Correlation] The method involves the following steps:\nStep 1 - Import data and extract metadata from file names\nStep 2 - Group individual channels from each image \nStep 3 - Measure colocalization\nStep 4 - Export the data", "[Expansion Microscopy TMEM55B and Myc-RILPL1 ... |
91,023 | Sanger Tree of Life Sample Homogenisation: Covaris cryoPREP® Automated Dry Pulverizer | 4 | dx.doi.org/10.17504/protocols.io.eq2lyjp5qlx9/v2 | https://www.protocols.io/view/sanger-tree-of-life-sample-homogenisation-covaris-c45pyy5n | Juan Pablo Narváez-Gómez, Haddijatou Mbye, graeme oatley, Michelle Strickland, Naomi Park, 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, Naomi Park, Caroline Howard
[DESCRIPTION]
This protocol describes the procedure for cryogenic homogenisation of tissue samples using the ... | ["[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... |
43,590 | Cell Culture and UV Cross-Linking | 4 | dx.doi.org/10.17504/protocols.io.bntemeje | https://www.protocols.io/view/cell-culture-and-uv-cross-linking-bntemeje | Clémentine Delan-Forino, David Tollervey | TITLE: Cell Culture and UV Cross-Linking
AUTHORS: Clémentine Delan-Forino, David Tollervey
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The RNA exosome complex functions in both the accurate processing and rapid degradation of many classes of RNA in eukaryotes and Archaea. Functional and structur... | ["[Growth and Cross-Linking of RNA–Exosome Subunit-His-TEV-ProteinA (HTP) Complexes]\nStreak out HTP-tagged and negative control strains from glycerol stocks onto YPD plates (or SD medium—leucine when required for plasmid maintenance) and incubate at for –.\n30 °C", "[Growth and Cross-Linking of RNA–Exosome Subunit-Hi... |
78,340 | In vitro GCase activity assay (total cell lysate) | 1 | dx.doi.org/10.17504/protocols.io.5qpvordxbv4o/v1 | https://www.protocols.io/view/in-vitro-gcase-activity-assay-total-cell-lysate-cqrcvv2w | Federico Bertoli, Michela Deleidi | TITLE: In vitro GCase activity assay (total cell lysate)
AUTHORS: Federico Bertoli, Michela Deleidi
[DESCRIPTION]
Glucocerebrosidase is a lysosomal enzyme that catalyzes the hydrolysis of glucosylceramide (GlcCer), a membrane glyco-sphingolipid, to ceramide and glucose. This assay detects GBA activity by using a flu... | ["[Sample Lysis] Suspend samples in 50 µL of 1% Triton extraction buffer.", "[Sample Lysis] Homogenize with a Dounce homogenizer for 25 strokes.", "[Sample Lysis] Rotate samples for 30 min at 4 °C.", "[Sample Lysis] Centrifuge at 13500 x g, 4 °C for 15 min.", "[Sample Lysis] Collect supernatants.", "[Substrate prepara... |
null | null | null | dx.doi.org/10.17504/protocols.io.dkr4v5 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This lysis buffer is strong enough for lysis most cell lines and wild enough to keep protein interactions. It has been tested on mouse embryonic stem cells, cancer cell lines and overexpressed cells. <br /><br />
[GUIDELINES]
<table style="height: 274px;" width="644">
<tbo... | [] |
51,745 | Preparation of Single Cell Suspension from Human Lung Tissue | 1 | dx.doi.org/10.17504/protocols.io.bwr9pd96 | https://www.protocols.io/view/preparation-of-single-cell-suspension-from-human-l-bwr9pd96 | Steven B. Wells, Peter A. Szabo, Basak Ural, Maya M.L. Poon | TITLE: Preparation of Single Cell Suspension from Human Lung Tissue
AUTHORS: Steven B. Wells, Peter A. Szabo, Basak Ural, Maya M.L. Poon
[DESCRIPTION]
This protocol describes a method for the isolation of the immune cells, structural and epithelial cells, and progenitors from human lung sections of about two grams. By... | ["[Preparing Mediums and Buffers] Create the following IMDM-FBS-PSQ Media in a 500 mL bottle of IMDM by using the table below: \n Component Volume (mL) Starting Conc. Final Conc.* IMDM 500 - - Penicillin-Streptomycin-Glutamine 5 100X 1X FBS 50 100% 10%", "[Preparing Mediums and Buffers] Creat... |
57,654 | HMW DNA extraction for amphipods | 4 | dx.doi.org/10.17504/protocols.io.b4iwqufe | https://www.protocols.io/view/hmw-dna-extraction-for-amphipods-b4iwqufe | Benoît Vacherie, Karine Labadie | TITLE: HMW DNA extraction for amphipods
AUTHORS: Benoît Vacherie, Karine Labadie
[DESCRIPTION]
Protocol adapted from Qiagen's genomic DNA handbook protocol for the HMW extraction of live or flash-freezed amphipods.
[GUIDELINES]
To preserve large DNA sizes, never use Vortex and only use Wide-Bore tips.
[STEPS]
SEC... | ["[Tissue homogenization] Prepare the lysis buffer by adding 3 µL of RNase A (100 mg/mL) to 1.5 ml of Buffer G2 per sample.", "[Tissue homogenization] place live or flash-freezed amphipod in 2ml douncer and add 1 ml of lysis buffer", "[Tissue homogenization] gently up and down 10 times with the piston", "[Tissue homog... |
null | null | null | dx.doi.org/10.17504/protocols.io.fgtbjwn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>This protocol is adapted from the Invitrogen Life Technologies Trizol manual. </p>
[BEFORE_START]
<ol>
<li>Prepare an <strong>RNase-free</strong> working area, wipe down barrels of micropipettes, use <strong>filter tips</strong> and RNase-free microcentrifuge tubes, and alwa... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.n3ddgi6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p><em>The MELD Project is an international collaboration aiming to create open-access, robust and generalisable tools for FCD detection. To this end, we will train a neural network classifier on MRI features from FCD patients from multiple centres worldwide.</em></p>
<p><strong... | [] |
35,038 | Lightsheet Tissue Intake - Photodocumentation and Tracking | null | dx.doi.org/10.17504/protocols.io.bef6jbre | https://www.protocols.io/view/lightsheet-tissue-intake-photodocumentation-and-tr-bef6jbre | Seth Currlin, Marda Jorgensen | TITLE: Lightsheet Tissue Intake - Photodocumentation and Tracking
AUTHORS: Seth Currlin, Marda Jorgensen
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>In order to track tissue position and orientation each sample is photographed when received for lightsheet microscopy (Figure 1, A). Large sa... | ["Photograph whole tissue; capture from various angles if possible. A dissection ruler or grid should accompany each photograph.", "Using a razor blade and forceps slice the tissue into sections approximately 2 mm wide. Try to slice in a continuous motion, while applying a gentle downward force.", "Set aside tissue sec... |
70,110 | Low Biomass, high contamination Illumina DNA prep using DNeasy PowerSoil (Pro) Kit | 4 | dx.doi.org/10.17504/protocols.io.6qpvr4ey3gmk/v1 | https://www.protocols.io/view/low-biomass-high-contamination-illumina-dna-prep-u-cgp6tvre | Tania Kurbessoian, Jason E Stajich, Sonia L. Ghose | TITLE: Low Biomass, high contamination Illumina DNA prep using DNeasy PowerSoil (Pro) Kit
AUTHORS: Tania Kurbessoian, Jason E Stajich, Sonia L. Ghose
[DESCRIPTION]
This is an addendum to the already optimized DNeasy PowerSoil Kit. This can also be applied to the PowerSoil Pro Kit.
Use this protocol for Low Biomass or ... | ["Add sample into the PowerBead tube.", "Add 60μL of Solution C1.", "Make sure the sample has not precipitated. If so, heat sample to 60ºC until precipitate is dissolved into solution.", "Vortex to mix and incubate at 65ºC for 10 minutes.", "Bead beat at \"homogenize\" setting: 90 seconds bead beating, 60 seconds rest,... |
63,998 | MEMBER_OWNER 002 | 1 | null | https://www.protocols.io/view/member-owner-002-caq6sdze | rober | TITLE: MEMBER_OWNER 002
AUTHORS: rober
[DESCRIPTION]
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Quisque hendrerit mauris quis nibh tincidunt pellentesque. Praesent congue justo vitae molestie dictum. Vivamus odio ipsum, consectetur eu nisi nec, posuere interdum metus. Class aptent taciti sociosqu ad li... | ["Lorem ipsum dolor sit amet, consectetur adipiscing elit. Quisque hendrerit mauris quis nibh tincidunt pellentesque. Praesent congue justo vitae molestie dictum. Vivamus odio ipsum, consectetur eu nisi nec, posuere interdum metus. Class aptent taciti sociosqu ad litora torquent per conubia nostra, per inceptos himenae... |
87,307 | Sanger Tree of Life Fragmented DNA clean up: Automated SPRI | 4 | dx.doi.org/10.17504/protocols.io.q26g7p1wkgwz/v1 | https://www.protocols.io/view/sanger-tree-of-life-fragmented-dna-clean-up-automa-czhjx34n | graeme oatley, Filipa Sampaio, Caroline Howard | TITLE: Sanger Tree of Life Fragmented DNA clean up: Automated SPRI
AUTHORS: graeme oatley, Filipa Sampaio, Caroline Howard
[DESCRIPTION]
This protocol describes the automated clean up and shorter fragment removal from fragmented DNA following the Sanger Tree of Life HMW DNA Fragmentation protocols, using PacBio AMPure... | ["[Laboratory protocol] Normalise the volumes of all sheared DNA samples to the sample with the largest volume.", "[Laboratory protocol] Set-up the KingFisher™ plates for the automated SPRI as detailed below:\n\n Plate namePlate typeReagent(s) requiredTip plateKingFisher‱ Apex 1 mL 96-well deep-well plateKingFisher‱ ... |
93,933 | Aggregation propensity of α-synuclein seeds in primary neurons | 4 | dx.doi.org/10.17504/protocols.io.81wgbxe13lpk/v1 | https://www.protocols.io/view/aggregation-propensity-of-synuclein-seeds-in-prima-c7ymzpu6 | Arpine Sokratian | TITLE: Aggregation propensity of α-synuclein seeds in primary neurons
AUTHORS: Arpine Sokratian
[DESCRIPTION]
This protocol describes the details of the treatment of primary hippocampal culture with α-synuclein fibrils or monomer protein. It also includes details of the collection of cell lysates for immunoblotting or... | ["Prepare primary hippocampal neurons according to protocol", "At DIV21 for 14 days of incubation or at DIV14 for 7 days of incubation culture media should be removed - aspirate the media", "Here are options to use the prepared cultures for the western-blot analysis or ELISA (step-case) or for the immunofluorescence", ... |
31,260 | Environmental DNA (eDNA) metabarcoding protocol for fish species | 1 | dx.doi.org/10.17504/protocols.io.bar4id8w | https://www.protocols.io/view/environmental-dna-edna-metabarcoding-protocol-for-bar4id8w | Omneya Ahmed, Tomas Larsson, Mats Töpel, Alexander Eiler | TITLE: Environmental DNA (eDNA) metabarcoding protocol for fish species
AUTHORS: Omneya Ahmed, Tomas Larsson, Mats Töpel, Alexander Eiler
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"> Environmental DNA metabarcoding universal primers targeting the hypervariable region of the 12S rRNA gene </div><... | ["DNA extraction can be performed using Qiagen DNeasy power water sterivex kit. The quality of the extracted DNA was estimated using Nanodrop. \n\nQiagen DNeasy power water sterivex kit: https://www.qiagen.com/se/resources/resourcedetail?id=c5fe7d5f-070a-4ebe-ac04-4bbf05a13e91&lang=en", "Perform the first PCR (triplica... |
45,186 | GM Covid-19 saliva test (v2) | 4 | null | https://www.protocols.io/view/gm-covid-19-saliva-test-v2-bqdams2e | TITLE: GM Covid-19 saliva test (v2)
AUTHORS:
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">GM Covid-19 saliva test is a RT-PCR test intended for qualitative detection of nucleic acids from SARS-CoV-2 in saliva specimen. The test is used for screening purpose under class of "research used only" (... | ["[Setup reaction]\nPrepare PCR master mixPrepare 100 reactions by adding 1ml Buffer into 1ml Enzyme. Aliquot 20ul into each PCR tube.", "[Setup reaction]\nSaliva-PrepSaliva is self-collected into any sterile tubes with screw cap and wide opening (Sanitize hands before and after saliva collection); Use disposable trans... | |
21,200 | Structured Interview for Protocol Use | null | dx.doi.org/10.17504/protocols.io.yxqfxmw | null | Drew Gitomer | TITLE: Structured Interview for Protocol Use
AUTHORS: Drew Gitomer
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a modification of Palinkas et al SIEU. Based on a lot of feelings and intuitions we thought that a 4 point scale would be super.</div><div class = "text-block">This article des... | [] |
93,161 | ssDNA2.0: Fill-in mix | 3 | dx.doi.org/10.17504/protocols.io.dm6gp3111vzp/v1 | https://www.protocols.io/view/ssdna2-0-fill-in-mix-c68hzht6 | Sarah Nagel, Anna Schmidt, Matthias Meyer | TITLE: ssDNA2.0: Fill-in mix
AUTHORS: Sarah Nagel, Anna Schmidt, Matthias Meyer
[DESCRIPTION]
Protocol for the preparation of Fill-in mix for automated single-stranded DNA library preparation using the ssDNA2.0 method (Gansauge et al. 2020).
References
Gansauge, M.-T., Aximu-Petri, A., Nagel, S., & Meyer, M. (2020).... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.invcde6 | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>We propose a Single-Strand Conformation Polymorphism (SSCP) methodology to recognize each species as an effective tool in <em>Diatraea</em> species identification.</p>
[STEPS]
?.
?.
?. | [] |
66,472 | Measurement of dissolved carbohydrate | 6 | dx.doi.org/10.17504/protocols.io.bp2l6168zvqe/v1 | https://www.protocols.io/view/measurement-of-dissolved-carbohydrate-cc6gszbw | Ying-Yu Hu, Zoe V. Finkel | TITLE: Measurement of dissolved carbohydrate
AUTHORS: Ying-Yu Hu, Zoe V. Finkel
[DESCRIPTION]
Here we describe a protocol to measure the dissolved carbohydrate, including total dissolved monosaccharides and total dissolved polysaccharides.
For total dissolved carbohydrate measurement, freeze-dried dissolved carbohydr... | ["[Sample collection] GFF filter is combusted for 240 min at 450 °C \nGlass filter holder is combusted for 120 min at 500 °C \nGlass filter funnel, flask and 10 mL centrifuge tubes are combusted for 360 min at 500 °C \n \nTube caps are acid-washed.", "[Sample collection] Filter microalgae sample and collect the fi... |
49,543 | Procedure for measuring extraction efficiency | 1 | null | https://www.protocols.io/view/procedure-for-measuring-extraction-efficiency-bumfnu3n | Krista Longnecker, Gretchen Swarr | TITLE: Procedure for measuring extraction efficiency
AUTHORS: Krista Longnecker, Gretchen Swarr
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Capturing dissolved organic matter from seawater using solid phase extraction is not 100% efficient. We use this protocol to quantify the amount of organic ... | ["[Procedure for measuring extraction efficiency]\nThis protocol starts with the eluent from a solid phase extraction resin. Dry down eluents in vials (all the way down, no solvent remaining!).\n8 mL", "[Procedure for measuring extraction efficiency]\nWhile drying down prepare EPA vials with MQ water and HCl.\n40 mL... |
40,086 | Database Preparation and Search for Protein Identification | 3 | dx.doi.org/10.17504/protocols.io.bjdwki7e | https://www.protocols.io/view/database-preparation-and-search-for-protein-identi-bjdwki7e | avinash.kale | TITLE: Database Preparation and Search for Protein Identification
AUTHORS: avinash.kale
[STEPS] | [] |
83,246 | Chloroform-free DNA Extraction - Ammonium Acetate Precipitation Method | 4 | dx.doi.org/10.17504/protocols.io.x54v9pekzg3e/v1 | https://www.protocols.io/view/chloroform-free-dna-extraction-ammonium-acetate-pr-cvinw4de | NERC Environmental Omics Facility (NEOF) Visitor Facility | TITLE: Chloroform-free DNA Extraction - Ammonium Acetate Precipitation Method
AUTHORS: NERC Environmental Omics Facility (NEOF) Visitor Facility
[DESCRIPTION]
A chloroform-free, cost-effective DNA extraction method for a variety of sample types.
[STEPS]
1. Add 250 µL Digsol buffer (see Materials for recipe) and 10 ... | ["Add 250 µL Digsol buffer (see Materials for recipe) and 10 µL to a lablelled 1.5ml tube.", "Tissue: Cut into small pieces (<1cm2) with a sterile razor blade on a sterile glass plate before adding to the 1.5mL tube.\nBlood: Centrifuge blood sample at 13,000rpm for about 1 min (to pellet sample).\nRemove sample from ... |
75,201 | Implant Surgery: Chronic recoverable Neuropixels in mice | 1 | null | https://www.protocols.io/view/implant-surgery-chronic-recoverable-neuropixels-in-cmn9u5h6 | Emily A Aery Jones | TITLE: Implant Surgery: 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 protocol... | ["[Prepare surgical tools and field] Sterilize tips of metal instruments, ground screw, and headbar in autoclave 25 min or hot bead sterilizer 5 s . Disinfect cotton swabs, toothpick, and a weigh boat under UV light 30 min .", "[Prepare surgical tools and field] Disinfect surgical field with 10% bleach. Lay absorbent ... |
62,780 | COI library preparation for Illumina MiSeq eDNA metabarcoding - rocky intertidal seawater samples | 1 | dx.doi.org/10.17504/protocols.io.kxygxzordv8j/v1 | https://www.protocols.io/view/coi-library-preparation-for-illumina-miseq-edna-me-b9i4r4gw | Mary McElroy | TITLE: COI library preparation for Illumina MiSeq eDNA metabarcoding - rocky intertidal seawater samples
AUTHORS: Mary McElroy
[DESCRIPTION]
This protocol describes library preparation for COI amplicon metabarcoding with the Illumina MiSeq system. Seawater samples were collected from California rocky intertidal habita... | ["[Amplicon PCR] Dilute primers to 5 uM in PCR water. Dilute BSA to 4 mg/ml in PCR water. Set up triplicate PCRs for each sample.", "[Amplicon PCR] Perform PCRs in 20 ul volumes with the following reaction chemistry:\n\n10 ul 2X AmpliTaq Gold 360 Master Mix (Applied Biosystems)\n0.75 ul 4 mg/ml bovine serum albu... |
85,828 | Basketball Exercise | 1 | null | https://www.protocols.io/view/basketball-exercise-cx3cxqiw | Ziyong Ma | TITLE: Basketball Exercise
AUTHORS: Ziyong Ma
[DESCRIPTION]
A simple basketball training plan.
[GUIDELINES]
Just try your best to finish it
[STEPS]
SECTION: Dribble Exercise
2. Ball Rubs
1 x 10 s
SECTION: Dribble Exercise
3. Single Leg Wraps
-Left 1 x 20 s
-Right 1 x 20 s
SECTION: Dribble Exercise
4. 3-3-3 Drib... | ["[Dribble Exercise] Ball Rubs\n1 x 10 s", "[Dribble Exercise] Single Leg Wraps\n-Left 1 x 20 s \n-Right 1 x 20 s", "[Dribble Exercise] 3-3-3 Dribble Drill\n 2 x 20 s \nPS: with variations", "[Dribble Exercise] Cone Dribbling\n1 x 3 min \n-with variations", "[Shooting Exercises] Form Shooting (one hand)\n-Left 1 x 20 s... |
87,737 | TST Nuclei Isolation with GentleMACS - 220301 | 4 | dx.doi.org/10.17504/protocols.io.dm6gp39z1vzp/v1 | https://www.protocols.io/view/tst-nuclei-isolation-with-gentlemacs-220301-czwzx7f6 | Sébastien Vigneau | TITLE: TST Nuclei Isolation with GentleMACS - 220301
AUTHORS: Sébastien Vigneau
[DESCRIPTION]
This protocol describes the process of nuclei isolation from frozen tissue. The protocol has been applied to frozen melanoma, breast, and lung metastases for the Human Tumor Atlas Network (HTAN) single-nuclei RNA-seq preparat... | ["Buffer Preparation\n\nPrepare the necessary buffers and solutions as outlined below:\n\n2x ST (50 mL stock solution can be prepared ahead of time and stored at room temperature)\n \n\nTST (2 mL should be prepared for each tissue sample)\n*10% Tween-20 can be prepared ahead of time and stored at 4ºC\n \n\nReagent\n\... |
50,930 | LPCA | 3 | dx.doi.org/10.17504/protocols.io.bvysn7we | https://www.protocols.io/view/lpca-bvysn7we | Kizito Ndihokubwayo, Jean Uwamahoro, Irénée Ndayambaje, Michael Ralph | TITLE: LPCA
AUTHORS: Kizito Ndihokubwayo, Jean Uwamahoro, Irénée Ndayambaje, Michael Ralph
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS] | [] |
88,717 | Barcode Composition by Overlap-Extension PCR | 1 | dx.doi.org/10.17504/protocols.io.ewov1q2p7gr2/v2 | https://www.protocols.io/view/barcode-composition-by-overlap-extension-pcr-c2vmye46 | Mathew Chu | TITLE: Barcode Composition by Overlap-Extension PCR
AUTHORS: Mathew Chu
[DESCRIPTION]
Traditionally, DNA barcodes are synthesised as random oligonucleotides. However, this leads to uncertainty regarding the ground truth of barcode sequences in the experimental setting. Without reference sequences, it is impossible to ... | ["[Single Stranded DNA Pools for Combinatorial Assembly] ssDNA oligos for combinatorial assembly can be ordered as a pool (oPool). For a final barcode of n units, each with m diversity, order a set of m different barcode sequences for each unit:\n \nwhere unit i (1 ≤ i ≤ n) consists of m barcodes flanked by left (L) an... |
19,558 | DOI document | null | dx.doi.org/10.17504/protocols.io.xcefite | null | Andrew Khramchenkov | TITLE: DOI document
AUTHORS: Andrew Khramchenkov
[STEPS]
?. | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.reid3ce | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>On June 14-17, 2018, the 23rd EHA conference was held in Sweden-Stockholm. The heavy research in the blood field took place. The development of new drugs in the field of acute leukemia has progressed rapidly. Among them, antibody-drug conjugates(<a href="https://www.creative-... | [] |
98,223 | Fiber Photometry Protocol | 0 | dx.doi.org/10.17504/protocols.io.eq2lyw39qvx9/v1 | https://www.protocols.io/view/fiber-photometry-protocol-db6p2rdn | Sasha Burwell | TITLE: Fiber Photometry Protocol
AUTHORS: Sasha Burwell
[DESCRIPTION]
This protocol details collection of fiber photometry from VTA dopamine neurons.
[GUIDELINES]
Recordings collected with a Tucker-Davis Technologies RZ10X and TDT Synapse software.
[STEPS]
SECTION: On every day of behavior (see Behavior protocol):
1... | ["[On every day of behavior (see Behavior protocol):] Photobleach the mono fiberoptic patchcords (Doric Lenses Inc., MFP_400/430/1100-0.57_1mm_FCM-MF1.25_LAF) (Synapse -> Preview Mode -> Fiber Bleaching) for at least 60 min, and up to 240 min, in both the 415nm and 465nm channels.\n\nThis can be done the night before t... |
53,104 | Illumina DNA Prep (M) Tagmentation Library Preparation for use on an Illumina MiSeq Sequencer | 1 | dx.doi.org/10.17504/protocols.io.bx4qpqvw | https://www.protocols.io/view/illumina-dna-prep-m-tagmentation-library-preparati-bx4qpqvw | Julie Haendiges, Narjol Gonzalez-Escalona, Ruth Timme, Maria Balkey | TITLE: Illumina DNA Prep (M) Tagmentation Library Preparation for use on an Illumina MiSeq Sequencer
AUTHORS: Julie Haendiges, Narjol Gonzalez-Escalona, Ruth Timme, Maria Balkey
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This procedure outlines the protocol for whole genome sequencing of bacter... | ["[Dilute and Tagment Input DNA]\nBring BLT (stored in refrigerator) and TB1 (stored in freezer) to room temperature. Ensure that BLT is stored upright at all times, so that the beads remain submerged in thebuffer", "[Dilute and Tagment Input DNA]\nLabel a 96-well PCR plate with the Run ID.", "[Dilute and Tagment Inpu... |
26,574 | RNA isolation from suspended animal cells, cDNA library construction, and RNA-Seq for gene expression analysis | 1 | dx.doi.org/10.17504/protocols.io.57ng9me | https://www.protocols.io/view/rna-isolation-from-suspended-animal-cells-cdna-lib-57ng9me | Tomoko Matsuda | TITLE: RNA isolation from suspended animal cells, cDNA library construction, and RNA-Seq for gene expression analysis
AUTHORS: Tomoko Matsuda
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is for RNA Isolation from suspended Chinese hamster ovary (CHO) cells. Wash cells once in 1× PBS... | ["Cells Maintenance", "CHO-S cells were grown in 20 ml of Gibco CD-CHO medium (Thermo Fisher Scientific, Waltham, MA, USA) containing 400 µL of 200 mM L-Alanyl-L-glutamine (final concentration: 4 mM; Sigma-Aldrich, St. Louis, MI, USA) and 40 µL of Gibco Anti-Clumping Agent (final concentration, 0.2% (v/v); Thermo Fishe... |
74,126 | Sugar Beet Tissue Collection for Genome Assembly and Annotation with Long Read Sequencing | 4 | null | https://www.protocols.io/view/sugar-beet-tissue-collection-for-genome-assembly-a-ckmnuu5e | olivia.todd | TITLE: Sugar Beet Tissue Collection for Genome Assembly and Annotation with Long Read Sequencing
AUTHORS: olivia.todd
[DESCRIPTION]
This protocol outlines the various types of tissue collection needed to follow the USDA-ARS Dorn lab protocol for Beta vulgaris crop wild relative genome sequencing. The annotation pipeli... | ["Follow the protocol below as written to isolate plant nuclei from 1-5g of dark treated tissue.\nhttps://15a13b02-7dac-4315-baa5-b3ced1ea969d.filesusr.com/ugd/5518db_90f751986a4a4e7bbc8e648d467507d2.pdf?index=true", "Check for quality and presence of necessary DNA size for sequencing (>15kb) using a Pippin Pulse, runn... |
null | null | null | dx.doi.org/10.17504/protocols.io.iiwccfe | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The procedures to determine the half-lives of proteins by pulse-chase analysis and cycloheximide blocking are well established. In the case of oligomeric proteins, these methods do not differentiate whether the stabilities of the monomeric versus oligomeric forms of the prote... | [] |
38,787 | Plasmid Extraction | 4 | null | https://www.protocols.io/view/plasmid-extraction-bh5bj82n | Hung Liang Pai, Huan Jui Chang | TITLE: Plasmid Extraction
AUTHORS: Hung Liang Pai, Huan Jui Chang
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used for extracting plasmid from E. coli DH5-Alpha strains. </div></div>
[STEPS]
?. [Preparation]
Set the dry bath incubator at
37 °C
?. [Preparation]
Prepare Presto™ M... | ["[Preparation]\nSet the dry bath incubator at\n37 °C", "[Preparation]\nPrepare Presto™ Mini Plasmid Kit", "[Preparation]\nTake out the centrifuge tube containing medium with bacteria that has been cultured overnight.", "[Protocol]\nCentrifuge the centrifuge tube under this condition - .\nCentrifuge: 15000 34, 6 min"... |
19,777 | U Cinn - Energy Expenditure Measurements | null | dx.doi.org/10.17504/protocols.io.xi9fkh6 | null | Patrick Tso | TITLE: U Cinn - Energy Expenditure Measurements
AUTHORS: Patrick Tso
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">
Oxygen consumption and carbon dioxide production is measured using indirect calorimetry. The Columbus... | ["Energy Expenditure by Oxymax Protocol (Columbus Instruments)1. Take Body Composition via NMR before you put animals in this experiment.\n2. Set up cages (this can be done at any time before starting an experiment)\n a. Weigh animals and place into Oxymax chambers\n b. Supply food and water\n c. Make sure c... |
null | null | null | dx.doi.org/10.17504/protocols.io.fctbiwn | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?. | [] |
71,507 | Monkeypox virus multiplexed PCR amplicon sequencing (PrimalSeq) | 1 | dx.doi.org/10.17504/protocols.io.5qpvob1nbl4o/v3 | https://www.protocols.io/view/monkeypox-virus-multiplexed-pcr-amplicon-sequencin-ch3tt8nn | Nicholas F.G. Chen*, Luc Gagne*, Matthew Doucette, Sandra Smole, Erika Buzby, Joshua Hall, Stephanie Ash, Rachel Harrington, Seana Cofsky, Selina Clancy, Curtis J Kapsak, Joel Sevinsky, Kevin Libuit, mallery.breban, Chrispin Chaguza, Nathan D. Grubaugh, Daniel J. Park, Glen R. Gallagher#, Chantal B.F. Vogels# | TITLE: Monkeypox virus multiplexed PCR amplicon sequencing (PrimalSeq)
AUTHORS: Nicholas F.G. Chen*, Luc Gagne*, Matthew Doucette, Sandra Smole, Erika Buzby, Joshua Hall, Stephanie Ash, Rachel Harrington, Seana Cofsky, Selina Clancy, Curtis J Kapsak, Joel Sevinsky, Kevin Libuit, mallery.breban, Chrispin Chaguza, N... | ["[Dilute and Pool Primers] Reagents:", "[Dilute and Pool Primers] If not already done, separate odd and even numbered primer pairs into two separate boxes. These will constitute the two pools", "[Dilute and Pool Primers] Label 164, 8-strip tubes with the corresponding odd-numbered primer name (e.g. 3 left)", "[Dilute ... |
43,141 | Protocol 2: PCR Wet Lab | 5 | null | https://www.protocols.io/view/protocol-2-pcr-wet-lab-bnddma26 | TITLE: Protocol 2: PCR Wet Lab
AUTHORS:
[DESCRIPTION]
<div class = "text-blocks"></div>
[STEPS]
?. DNA ExtractionDNA Extraction: Saliva (Bento lab) This protocol extracts DNA from Saliva using a microcentrifuge and thermocycler. The microcentrifuge separates the cells in the sample into a pellet at the bottom of ... | ["DNA ExtractionDNA Extraction: Saliva (Bento lab) This protocol extracts DNA from Saliva using a microcentrifuge and thermocycler. The microcentrifuge separates the cells in the sample into a pellet at the bottom of the microcentrifuge tube. Extra liquid is drawn out of the microcentrifuge tube. Cells are then heated... | |
79,067 | Single-cell dissociation of Drosophila melanogaster pupal tarsi | 4 | dx.doi.org/10.17504/protocols.io.x54v9dzbmg3e/v1 | https://www.protocols.io/view/single-cell-dissociation-of-drosophila-melanogaste-crf3v3qn | Ben R. Hopkins, Olga Barmina, Artyom Kopp | TITLE: Single-cell dissociation of Drosophila melanogaster pupal tarsi
AUTHORS: Ben R. Hopkins, Olga Barmina, Artyom Kopp
[DESCRIPTION]
This protocol outlines a step-by-step guide to generating single-cell suspensions of Drosophila melanogaster pupal tarsi for use in 10x single-cell transcriptome profiling. This proto... | ["[Collecting, sexing, and ageing pupae] Collect white prepupae. Individuals should meet the P1 aging criteria laid out by Bainbridge and Bownes (1981): the pupae should be white or cream coloured, have stopped moving completely, and display everted anterior spiracles.", "Identify individuals of the correct sex. Place ... |
49,128 | Initial Rapid Pathology Assessment of Kidney Tissue | 1 | dx.doi.org/10.17504/protocols.io.bt8gnrtw | https://www.protocols.io/view/initial-rapid-pathology-assessment-of-kidney-tissu-bt8gnrtw | Jamie Allen, Carrie Romer, Elizabeth Neumann, Maya Brewer, Haichun Yang, Jeff Spraggins, Danielle Gutierrez | TITLE: Initial Rapid Pathology Assessment of Kidney Tissue
AUTHORS: Jamie Allen, Carrie Romer, Elizabeth Neumann, Maya Brewer, Haichun Yang, Jeff Spraggins, Danielle Gutierrez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Scope:</div><div class = "text-block">Prepare formalin fixed tissue with fr... | ["Tissue is embedded in protocol: dx.doi.org/10.17504/protocols.io.br4fm8tn", "Section samples at 5 µm on a microtome.", "PAS stain tissue sections with protocol: dx.doi.org/10.17504/protocols.io.buaknscw", "Scan slides with brightfield scanner (Leica) and save as .tiff or .jpg", "Place saved images on QuPath for analy... |
32,472 | PCR amplification of long GC-rich DNA targets | 1 | dx.doi.org/10.17504/protocols.io.bbxyippw | https://www.protocols.io/view/pcr-amplification-of-long-gc-rich-dna-targets-bbxyippw | Nadia Assal, Min Lin | TITLE: PCR amplification of long GC-rich DNA targets
AUTHORS: Nadia Assal, Min Lin
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol allows the amplification of long and high GC content genes by PCR without the need for many optimizations. In this protocol, the</span><span style = ... | ["Extract M. bovis genomic DNA using according to the manufacturer’s instructions for Gram-positive bacteria. Use 5 ng/µl of genomic DNA was used in each reaction", "Prepare the master mix for the polymerase enzyme as follows: AB1Componentvolume in µl2Milliq Water29.53Buffer104DNTPs (2.5mM)45DMSO2.56Primers Mix\... |
25,251 | Marchantia spores sterilisation | null | dx.doi.org/10.17504/protocols.io.4wbgxan | null | Linda Silvestri, Eftychis Frangedakis, Marius Rebmann, Susana Sauret-Gueto | TITLE: Marchantia spores sterilisation
AUTHORS: Linda Silvestri, Eftychis Frangedakis, Marius Rebmann, Susana Sauret-Gueto
[STEPS]
?. Add one Milton tablet into 25 mL of sterile water to prepare the "sterilization solution".
?. Add the sporangia into a 1.5 mL centrifuge tube and add 0.5 mL of sterilization solution in... | ["Add one Milton tablet into 25 mL of sterile water to prepare the \"sterilization solution\".", "Add the sporangia into a 1.5 mL centrifuge tube and add 0.5 mL of sterilization solution into the tube (B in Figure)", "Use sterile metal tweezers to crush the sporangia (C in Figure).", "Place a 40 μM cell strainer into a... |
31,227 | Optical mapping preps for Petunia spp. | null | dx.doi.org/10.17504/protocols.io.baq3idyn | null | Elena Hilario | TITLE: Optical mapping preps for Petunia spp.
AUTHORS: Elena Hilario
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Optical mapping technologies assist the assembly of large and complex genomes. Although protocols for preparing this kind of samples are now conveniently available as kits, some plant... | ["[Tissue Fixation]\nRemove ~ and place them in a 50 mL Falcon tube containing ~. Attach the green screened cap and slowly add more Fixing solution (total volume 60 mL).Remove all the air bubbles by tapping the tube but keeping it upright. Close the tube with its own cap and incubate on ice.\nDo the tissue fixation a... |
63,409 | Lumina Luxe Face Cream Reviews Best Anti Aging Cream for Glamorous Look! | 3 | dx.doi.org/10.17504/protocols.io.81wgb69p1lpk/v1 | https://www.protocols.io/view/lumina-luxe-face-cream-reviews-best-anti-aging-cre-b96rr9d6 | Lumina Luxe Face Cream | TITLE: Lumina Luxe Face Cream Reviews Best Anti Aging Cream for Glamorous Look!
AUTHORS: Lumina Luxe Face Cream
[DESCRIPTION]
Product Name: Lumina Luxe Face Cream
Category: FACE SKIN CARE CREAM
Price: $8 (for 1 box)
Official Website: Click Here
[STEPS] | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.cqqvvv | null | null | TITLE: No Title
AUTHORS:
[STEPS]
?.
?.
?.
?.
?. | [] |
20,958 | Cell Hashing | null | dx.doi.org/10.17504/protocols.io.yp6fvre | null | Brenton Paolella | TITLE: Cell Hashing
AUTHORS: Brenton Paolella
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is for performing Cell Hashing only. </div><div class = "text-block">Sample multiplexing and super-loading on single cell RNA-sequencing platforms.</div><div class = "text-block"><a style = "t... | ["[Cell staining for Drop-seq or 10x Genomics]\nObtain all single cell suspensions from different samples/conditions that will be multiplexed in the run. Keep samples in separate tubes until after cell hashing and shortly before loading cells into the single cell RNA-seq instrument. When aiming to super-load the same s... |
49,233 | Human intestinal cell dissociation suitable for multi-omics single-cell assays | 4 | dx.doi.org/10.17504/protocols.io.bubrnsm6 | https://www.protocols.io/view/human-intestinal-cell-dissociation-suitable-for-mu-bubrnsm6 | Astrid Kosters, Junkai Yang, Ann Dodd, Mackenzie White, Greg Gibson, Subra Kugathasan, Peng Qiu, Eliver Ghosn | TITLE: Human intestinal cell dissociation suitable for multi-omics single-cell assays
AUTHORS: Astrid Kosters, Junkai Yang, Ann Dodd, Mackenzie White, Greg Gibson, Subra Kugathasan, Peng Qiu, Eliver Ghosn
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">We developed a protocol for the preparation ... | ["Chop tissue into small pieces with a razor blade in def-RPMI/3%NBCS/EDTA/DTT media in a 6 cm dish, on ice.", "Transfer tissue solution to 15 mL conical (use 1 mL pipet).", "Vortex the tissue solution, and incubate at RT for 5 min, vortexing intermittently.", "Fill the 15 mL conical with def-RPMI/3%NBCS.", "Spin for 5... |
91,233 | Cartilage staining | 4 | null | https://www.protocols.io/view/cartilage-staining-c5b9y2r6 | Satheeswaran Balasubramanian, Ekambaram Perumal | TITLE: Cartilage staining
AUTHORS: Satheeswaran Balasubramanian, Ekambaram Perumal
[DESCRIPTION]
The Alcian Blue staining technique is widely used among developmental biologists to observe the embryonic development of cartilage and bone structures in embryos and complete zebrafish larvae. Alcian blue is a positively c... | ["[Larval fixation] At the desired stage, the larvae for staining are taken and washed once in PBS for 5 minutes.", "[Larval fixation] The larvae were euthanized using the cold shock method (Keep at 4oC for 5-10 minutes).", "[Larval fixation] Transfer the euthanized larvae into 4% PFA and keep it in the rocker for 2 ho... |
55,026 | NAN KB Demo: Data download | 5 | null | https://www.protocols.io/view/nan-kb-demo-data-download-bzysp7we | Abby Moore | TITLE: NAN KB Demo: Data download
AUTHORS: Abby Moore
[DESCRIPTION]
The purpose of this protocol is to describe how data may be downloaded from "our project."
The scope of this protocol extends to any instance where a user must download data from a spectrometer that is a part of "our project."
[BEFORE_START]
For t... | ["[Data download] Select the appropriate case below to proceed.", "[Data download] Open a terminal in", "[Data download] Copy your data from the spectrometer using the following command:", "[Data download] You will be asked for your account password - type this in and hit enter, your download should commence immediatel... |
58,022 | Differentiation of iPSC into Microglia-Like Cells (iMGL) | 1 | dx.doi.org/10.17504/protocols.io.q26g7bwqklwz/v3 | https://www.protocols.io/view/differentiation-of-ipsc-into-microglia-like-cells-b4weqxbe | Abhirami Kannan Iyer, Emma Danhash, Fabia Filipello, Jacob Marsh, Rj Martinez, Celeste M M. Karch | TITLE: Differentiation of iPSC into Microglia-Like Cells (iMGL)
AUTHORS: Abhirami Kannan Iyer, Emma Danhash, Fabia Filipello, Jacob Marsh, Rj Martinez, Celeste M M. Karch
[DESCRIPTION]
This protocol outlines the derivation of Hematopoietic Progenitor Cells and differentiation of iMGLs using iPSC cultures. This pr... | ["[iPSCs Culture] Thaw and culture iPSC line per the following protocol:", "[iPSCs Aggregate Plating] Once iPSCs are 70-80% confluent in 2-3 wells of a 6-well tissue culture plate, passage and plate the iPSCs as aggregates", "[iPSCs Aggregate Plating] Coat a 6-well tissue culture plate with Matrigel for a least 60 min ... |
92,335 | Patient PBMC flow cytometry | 4 | dx.doi.org/10.17504/protocols.io.n92ldm688l5b/v1 | https://www.protocols.io/view/patient-pbmc-flow-cytometry-c6epzbdn | rebeccawallings | TITLE: Patient PBMC flow cytometry
AUTHORS: rebeccawallings
[DESCRIPTION]
Patient PBMC flow cytometry
[STEPS]
1. 1 x 106 PBMCs were taken for flow cytometry and transferred to a v-bottom 96-well plate
(Sigma, CLS3896-48EA) and centrifuged at 300x g for 5 minutes at 4°C.
Cells were resuspended in 50 µL of PBS contain... | ["1 x 106 PBMCs were taken for flow cytometry and transferred to a v-bottom 96-well plate\n(Sigma, CLS3896-48EA) and centrifuged at 300x g for 5 minutes at 4°C.\n\nCells were resuspended in 50 µL of PBS containing diluted fluorophore-conjugated antibodies and incubated in the dark at 4°C for 20 minutes. Cells were cent... |
42,463 | ELISA for assessing the burden of Neutrophil Extracellular Traps (NETs) in clinical serum samples. | 4 | dx.doi.org/10.17504/protocols.io.bmp7k5rn | https://www.protocols.io/view/elisa-for-assessing-the-burden-of-neutrophil-extra-bmp7k5rn | kathryn.hally | TITLE: ELISA for assessing the burden of Neutrophil Extracellular Traps (NETs) in clinical serum samples.
AUTHORS: kathryn.hally
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol steps through the ELISA procedure for detecting three NET-specific biomarkers: 1) myeloperoxidase-DNA (MPO-D... | ["[Solutions to be prepared for ELISAs.]\nFor Day 1:Coating buffer:\n[1x PBS]", "[ELISA day 2.]\nThoroughly remove the capture antibody by flicking off the solution and banging each plate face down on paper towels. Add to each well and incubate for . Flick and bang again. Repeat another four times (five washes in to... |
78,863 | Pathogen-Oriented Low-cost Assembly & Re-sequencing on Opentrons (POLARtron): An automation-friendly highly sensitive and high-throughput SARS-CoV-2 diagnostic based on whole genome sequencing | 4 | dx.doi.org/10.17504/protocols.io.81wgbp8jqvpk/v2 | https://www.protocols.io/view/pathogen-oriented-low-cost-assembly-amp-re-sequenc-cq9pvz5n | Per A. Adastra, Neva C. Durand, Namita Mitra, Saul Godinez, Ragini Mahajan, Alyssa Blackburn, Zane Colaric, Joshua W. M. Theisen, David Weisz, Olga Dudchenko, Andreas Gnirke, Suhas S.P. Rao, Parwinder Kaur, Erez Lieberman Aiden, Aviva Presser Aiden | TITLE: Pathogen-Oriented Low-cost Assembly & Re-sequencing on Opentrons (POLARtron): An automation-friendly highly sensitive and high-throughput SARS-CoV-2 diagnostic based on whole genome sequencing
AUTHORS: Per A. Adastra, Neva C. Durand, Namita Mitra, Saul Godinez, Ragini Mahajan, Alyssa Blackburn, Zane Colaric... | ["[RNA Extraction] For each saliva sample recieved add equal volume saliva and 2X DNA/RNA Shield from the Quick-DNA/RNA Viral magbead kit and vortex. Centrifuge the samples at 500 rpm, 5 min to bring down debris.", "[RNA Extraction] Without disturbing the pellet, transfer 25 µL of saliva sample and 1X DNA/RNA to the ... |
29,287 | High-quality RNA purification with on-column DNase treatment from tissue specimens | null | dx.doi.org/10.17504/protocols.io.8ufhwtn | null | Magda Bletsa, Antonios Fikatas, Yiqiao Li, Sophie Gryseels, Jan Felix Drexler, Philippe Lemey | TITLE: High-quality RNA purification with on-column DNase treatment from tissue specimens
AUTHORS: Magda Bletsa, Antonios Fikatas, Yiqiao Li, Sophie Gryseels, Jan Felix Drexler, Philippe Lemey
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol can be used for total RNA purification from ... | ["[Sample homogenisation]\nAdd RLT Buffer to the Precellys lysate tubes.\n600 µl", "[Sample homogenisation]\nExcise a lentil-sized piece of tissue (maximum amount of for RNAlater stabilized tissues and for fresh or frozen tissues) and transfer it quickly to the lysate tubes. Make sure that all tissues are immersed in... |
39,590 | Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and SARS-CoV-2 (4S)" method | 4 | dx.doi.org/10.17504/protocols.io.biwekfbe | https://www.protocols.io/view/direct-wastewater-rna-capture-and-purification-via-biwekfbe | Oscar Whitney, Basem Al-Shayeb, Alex Crits-Cristoph, Mira Chaplin, Vinson Fan, Hannah Greenwald, Adrian Hinkle, Rose Kantor, Lauren Kennedy, Anna Maurer, Robert Tjian, Kara L. Nelson, UC Berkeley Wastewater-based epidemiology consortium | TITLE: Direct wastewater RNA capture and purification via the "Sewage, Salt, Silica and SARS-CoV-2 (4S)" method
AUTHORS: Oscar Whitney, Basem Al-Shayeb, Alex Crits-Cristoph, Mira Chaplin, Vinson Fan, Hannah Greenwald, Adrian Hinkle, Rose Kantor, Lauren Kennedy, Anna Maurer, Robert Tjian, Kara L. Nelson, UC Berkeley Was... | ["[Sample preparation, RNA preservation and particle lysis]\nSpike a known volume and titer of bovine coronavirus (bCoV) into the wastewater sample as a recovery efficiency control. Agitate sample to fully mix bCoV or other spiked-in controls with the wastewater sample.\nOther recovery controls can be used instead of b... |
81,551 | High molecular weight DNA extraction for marine macroalgal tissue | 4 | dx.doi.org/10.17504/protocols.io.14egn2dnpg5d/v1 | https://www.protocols.io/view/high-molecular-weight-dna-extraction-for-marine-ma-ctvpwn5n | Malia Moore, Taylor S. Steele | TITLE: High molecular weight DNA extraction for marine macroalgal tissue
AUTHORS: Malia Moore, Taylor S. Steele
[DESCRIPTION]
This protocol details high molecular weight DNA extraction for marine macroalgal tissue. Marine macroalgae contain a variety of unique cell wall components including sulfated polysaccharides an... | ["[Lyophilizing algal tissue] Flash-freeze algal tissue in liquid nitrogen (target ≥5 g wet tissue).", "[Setting up the DNA extraction] Prepare desired volume of Carlson lysis buffer (100 millimolar (mM) Tris-HCl, pH 9.5, 2% CTAB, 1.4 Molarity (M) NaCl, 1% PEG 8000, 20 millimolar (mM) EDTA) and mix 1440 min on a magnet... |
29,666 | Enrichment of a specific polyadenylated RNA for nanopore direct RNA sequencing (RNA SPACE) | null | dx.doi.org/10.17504/protocols.io.88ahzse | null | Paul MK. Gordon | TITLE: Enrichment of a specific polyadenylated RNA for nanopore direct RNA sequencing (RNA SPACE)
AUTHORS: Paul MK. Gordon
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This RNA Sequence Picking After Cutting Enzymatically (RNA SPACE) protocol is intended to enrich for a specific polyadenyla... | ["[Oligonucleotide design]\nHave the three oligos synthesized (RE oligo, RTA Oligos A & B), by designing your own using the open source software and your reference data.", "[Enzymatic cleavage of target RNA]\nIn the same tube, perform 3h or overnight restriction digest according to the NEB protocol for your enzyme, e.g... |
83,141 | SynBot Protocols | 2 | dx.doi.org/10.17504/protocols.io.3byl4qewjvo5/v1 | https://www.protocols.click/view/synbot-protocols-cvfdw3i6 | Justin T Savage, Juan Ramirez, Dolores Irala, Cagla Eroglu | TITLE: SynBot Protocols
AUTHORS: Justin T Savage, Juan Ramirez, Dolores Irala, Cagla Eroglu
[DESCRIPTION]
Protocols related to the paper SynBot: An open-source image analysis software for automated quantification of synapses. Includes details of rat neuron and astrocyte culture, in vitro synapse staining, in vivo syna... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.qxfdxjn | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
<p>The purinosome has been observed in a broad spectrum of cells, but some studies claim that it is an artefact of the constructs used for visualization or stress granules resulting from the exposure of cells to nutrient-reduced growth media. Both may be true depending on the me... | [] |
94,482 | MBP-Clu-tail purification from Escherichia coli cells | 1 | dx.doi.org/10.17504/protocols.io.6qpvr35xzvmk/v1 | https://www.protocols.io/view/mbp-clu-tail-purification-from-escherichia-coli-ce-c8hszt6e | Andreas Bracher, F Ulrich Hartl | TITLE: MBP-Clu-tail purification from Escherichia coli cells
AUTHORS: Andreas Bracher, F Ulrich Hartl
[DESCRIPTION]
This protocol details how to efficiently purify the fusion protein Maltose binding protein (MBP)-Clu-tail (204-238) from Escherichia coli.
[STEPS]
SECTION: His6-Ubiquitin-GFP-Clu-tail expression and cel... | ["[His6-Ubiquitin-GFP-Clu-tail expression and cell lysis] Express MBP-Clu-tail in E. coli Bl21 (DE3) codon+RIL cells cultured in 1 L LB Medium containing 2 1655 glucose at 37 °C with 1 millimolar (mM) IPTG during 120 min.", "[His6-Ubiquitin-GFP-Clu-tail expression and cell lysis] Centrifuge culture and keep pellet.", "... |
36,796 | Coating Slides with Gelatin | null | dx.doi.org/10.17504/protocols.io.bf64jrgw | https://www.protocols.io/view/coating-slides-with-gelatin-bf64jrgw | Allen Institute for Brain Science | TITLE: Coating Slides with Gelatin
AUTHORS: Allen Institute for Brain Science
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The protocol describes how 1x3 glass microscope slides are coated with gelatin to improve adherence of fixed adult mouse brain sections or other tissue to slides.</div><div c... | [] |
null | null | null | dx.doi.org/10.17504/protocols.io.c8bzsm | null | null | TITLE: No Title
AUTHORS:
[DESCRIPTION]
This is a very simple protocol showing how to extract haemolymph from adult Drosophila melanogaster. (Based on protocols from Sigma Aldrich).
[GUIDELINES]
<span class="s1"><strong>Materials:</strong></span> <br /><span class="s1">-0.5 μl capillaries with adequate suctio... | [] |
47,103 | Electroporation of Cas9 protein into human pluripotent stem cells | 1 | dx.doi.org/10.17504/protocols.io.br87m9zn | https://www.protocols.io/view/electroporation-of-cas9-protein-into-human-pluripo-br87m9zn | Jiuchun Zhang, Harper JW | TITLE: Electroporation of Cas9 protein into human pluripotent stem cells
AUTHORS: Jiuchun Zhang, Harper JW
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the electroporation of Cas9 protein into human pluripotent stem cells.</div></div>
[STEPS]
?. Add to a sterile 1.5 ml t... | ["Add to a sterile 1.5 ml tube. Add . Then add . Pipet up and down to mix. Let it sit at for . This is enough for 2 transfections (== one 6 well).\n[buffer R ]\n[purified Cas9 protein (2mg/ml)]\n[sgRNA]\n0 Room temperature", "While waiting for the Cas9 to bind to sgRNA, individualize cells with Accutase. Neutralize A... |
49,968 | Human breast tissue dissociation and FACS vs Flowmi processing for scRNA-Seq | 4 | dx.doi.org/10.17504/protocols.io.bu2qnydw | https://www.protocols.io/view/human-breast-tissue-dissociation-and-facs-vs-flowm-bu2qnydw | Maren Pein, smallya , Quy Nguyen, Jacob Insua-Rodríguez | TITLE: Human breast tissue dissociation and FACS vs Flowmi processing for scRNA-Seq
AUTHORS: Maren Pein, smallya , Quy Nguyen, Jacob Insua-Rodríguez
[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Single cell RNA-Seq of human breast tissue requires tissue dissociation into viable single cell suspens... | ["Initial Tissue PreparationTransfer breast tissue specimen to 150 x 22 mm cell culture dish. Remove medium and wash 3 times with 50-100 mL ice-cold PBS.Optional: If histological analysis is desired, separate tissue pieces and process as desired.", "Mechanical DigestionUsing forceps and scalpels, remove soft, white/yel... |
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