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81 results for “Pooled screen”
Data for Stable isotope composition of long and short term carbon pools can screen drought tolerance in cassava
<p>This repository contains data and scripts to reproduce results that are presented in the article: Van Laere, J., Martinez Maya, M.A., Selvaraj M.G., Becerra Lopez-Lavalle, L.A., Guzman, D., Casas, J.A., Merckx, R., Hood-Nowotny, R., Dercon, G. (2024)<strong> Stable isotope composition of long and short term carbon pools can screen drought tolerance in cassava</strong>. <em>Field Crops Research. </em>https://doi.org/10.1016/j.fcr.2024.109586</p>
Data and processing scripts for PRISM barcode sequencing data used in "Massively parallel pooled screening reveals genomic determinants of nanoparticle-cell interactions"
<p>Sequencing data for the PRISM barcodes generated after nano-particle treatment is presented in this repository alongside the code to process the sequencing counts to generate the binning probabilities and weighted scores. <br> <br> For the details please see the original publication or the bioarxiv preprint: https://doi.org/10.1101/2021.04.05.438521<br> <br> The raw data is provided in PILOT_DATA_COUNTS.csv and EXPERIMENT_DATA_COUNTS.csv files, for the pilot and the actual experiment. <br> <br> For each of these files an R script is provided to process them, along with the output of the scripts (PILOT_DATA_PROBABILITIES.csv and EXPERIMENT_DATA_PROBABILITIES.csv)</p>
A genome-wide optical pooled screen reveals regulators of antiviral responses
<p>Supplementary Datasets for "A genome-wide optical pooled screen reveals regulators of antiviral responses"</p> <p><strong>Supplementary Dataset 1. </strong>Mean per-gene extracted features for all channels of genome-wide screen</p> <p><strong>Supplementary Dataset 2. </strong>Features from single cells in secondary antibody screen</p> <p><strong>Supplementary Dataset 3. </strong>Features from single cells in secondary reporter screen</p> <p><strong>Supplementary Dataset 4. </strong>IRF3 translocation scores from primary and secondary IRF3 antibody and IRF3 reporter screens (the latter upon both Sendai virus and VSV infection) and SeV intensity scores from secondary antibody screen.</p> <p><strong>Supplementary Dataset 5. </strong>Peroxisome and Sendai virus feature scores from genome-wide screen</p>
Data from: Pooled genome-wide CRISPR activation screening for rapamycin resistance genes in Drosophila cells
<p>Loss-of-function and gain-of-function genetic perturbations provide valuable insights into gene function. In <em>Drosophila</em> cells, while genome-wide loss-of-function screens have been extensively used to reveal mechanisms of a variety of biological processes, approaches for performing genome-wide gain-of-function screens are still lacking. Here, we describe a pooled CRISPR activation (CRISPRa) screening platform in <em>Drosophila</em> cells and apply this method to both focused and genome-wide screens to identify rapamycin resistance genes. The screens identified three genes as novel rapamycin resistance genes: a member of SLC16 family of monocarboxylate transporters (<em>CG8468)</em>, a member of the lipocalin protein family (<em>CG5399</em>), and a zinc finger C2H2 transcription factor (<em>CG9932</em>). Mechanistically, we demonstrate that <em>CG5399</em> overexpression activates the RTK-Akt-mTOR signaling pathway and that activation of insulin receptor (InR) by <em>CG5399</em> requires cholesterol and clathrin-coated pits at the cell membrane. This study establishes a novel platform for functional genetic studies in <em>Drosophila</em> cells.</p>
Large-scale saliva pooling as a screening strategy to control transmission_raw data
<p>This dataset include the raw data of our experience after building a bespoke laboratory to control critical areas by pooling samples of saliva. From August 2020 to February 2022; 928,528 individual self-samples of saliva were processed in 52,580 pools, 4,935 of which were positive and helped us detect 5,806 nonsymptomatic individuals. </p> <p>The dataset was collected directly from the laboratory information system and was processed to delete the columns with sensitive information.</p> <p>The Dataset was charged as XLSX file and only need a compatible software.</p> <p>To facilitate the understanding of the data set, which uses the Galician language and an internal nomenclature of our laboratory, we include a sheet named "description" and a README file in which it defines the terms used and their equivalence with those used in the article.</p>
Data from: Pooled genome-wide CRISPR activation screening for rapamycin resistance genes in Drosophila cells
Open the record for dataset details and reuse information.
CRISPuRe-seq: pooled screening of barcoded ribonucleoprotein reporters reveals regulation of RNA polymerase III transcription by the Integrated Stress Response via mTOR
<p>NAR_Data_Package.zip contains the data required for generating figures, including original gel images for western blots and a step-by-step protocol for CRISPuRe-seq.</p> <p>SupplementaryData.xlsx contains all of the Supplemental Data directly referred to in the manuscript.</p> <p>Plasmid maps.zip contains plasmid maps for constructs used in the manuscript in genbank format.</p> <p>Scripts.zip contains the scripts used for screen processing with a text file explaining their usage.</p> <p>Look_Up_Table.zip contains the look-up-table for decoding barcode and sgRNA pairings.</p>
Pooled CRISPR Screening of High-content Cellular Phenotypes by Ghost Cytometry_01
<p>Pooled CRISPR screening of high-content cellular phenotypes by ghost cytometry (NFkB NGS data, conventional flow cytometer data, Amnis data)</p>
Pooled CRISPR Screening of High-content Cellular Phenotypes by Ghost Cytometry_02
<p>Pooled CRISPR Screening of High-content Cellular Phenotypes by Ghost Cytometry (Macrophage NGS data)</p>
Discovery of target genes and pathways of blood trait loci using pooled CRISPR screens and single cell RNA sequencing
GEO Series GSE171452. Homo sapiens. 28 samples. Type: Other.
Dissecting immune circuits by linking CRISPR pooled screens with single cell RNA-seq [SET2]
GEO Series GSE90487. Mus musculus. 8 samples. Type: Other.
Pooled CRISPR screens with imaging on microRaft arrays reveals stress granule-regulatory factors
GEO Series GSE139815. Homo sapiens. 107 samples. Type: Other.
Genome-wide pooled CRISPR knockout screen for novel regulators of macrophage efferocytosis.
GEO Series GSE212008. Mus musculus. 15 samples. Type: Other.
Pooled CRISPR screening in pancreatic cancer cells implicates co-repressor complexes as a cause of multiple drug resistance via regulation of epithelial-to-mesenchymal transition [ChIP-seq]
GEO Series GSE158540. Homo sapiens. 10 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
CRISPR-GEMM pooled mutagenic screening identifies KMT2D as a major modulator of immune checkpoint blockade (ATAC-Seq)
GEO Series GSE151226. Mus musculus. 12 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Scalable, compressed phenotypic screening using pooled perturbations (PDAC screens)
GEO Series GSE267243. Homo sapiens. 54 samples. Type: Expression profiling by high throughput sequencing.
Accurate quantification of CRISPR effects in pooled FACS screens using Waterbear
GEO Series GSE242880. Homo sapiens; synthetic construct. 67 samples. Type: Other.
CRISPR-GEMM pooled mutagenic screening identifies KMT2D as a major modulator of immune checkpoint blockade
GEO Series GSE151227. Mus musculus. 18 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Pooled CRISPR Screening Identifies m6A as a Positive Regulator of Macrophage Activation [m6A-RIP-seq]
GEO Series GSE162254. Mus musculus. 8 samples. Type: Methylation profiling by high throughput sequencing.
Targeting T cell plasticity by pooled single cell CRISPR-screening in preclinical models of kidney and gut inflammation
GEO Series GSE267740. Mus musculus; Homo sapiens. 56 samples. Type: Expression profiling by high throughput sequencing; Other.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.