GSM7328891: Rat CD4+ T-MBP cells with validation library, spleen, rep... - SRA

SRX20301955: GSM7328891: Rat CD4+ T-MBP cells with validation library, spleen, rep R1; Rattus norvegicus; OTHER
1 ILLUMINA (Illumina HiSeq 1500) run: 16.3M spots, 1.2G bases, 669.3Mb downloads

External Id: GSM7328891_r1

Submitted by: Institute for Clinical Neuroimmunology, Biomedical Center, University Hospital of the Ludwig-Maximilians University Munich

Study: Genome wide (GW) and validation CRISPR screens on encephalitogenic CD4+ T cell migration into the CNS

PRJNA971638 • SRP437278 • All experiments • All runs

show Abstracthide Abstract

To identify genes driving encephalitogenic CD4+ T cell migration into the CNS, we performed a genome-wide CRISPR screen and a subsequent validation screen For the genome-wide CRISPR screen, up to 4 sgRNA per gene and 800 non targeted controls were included, for a total of 87690 individual sgRNAs, and for the validation screen, up to 6 sgRNA per gene and 241 non targeted controls for a total of 12000 individual sgRNAs Overall design: Comparison of sgRNA distribution by pairwise comparisons across blood, spleen, spinal cord leptomeninges and spinal cord parenchyma

Sample: Rat CD4+ T-MBP cells with validation library, spleen, rep R1

SAMN35052127 • SRS17627811 • All experiments • All runs

Organism: Rattus norvegicus

Library:

Name: GSM7328891

Instrument: Illumina HiSeq 1500

Strategy: OTHER

Source: GENOMIC

Selection: other

Layout: SINGLE

Construction protocol: The spleen was dissected and homogenized by passing through a metal strainer. Erythrocytes were removed by treating with ACK buffer for 3 min on ice and CD4+ T cells were enriched using the EasySep™ Rat CD4+ T Cell Isolation Kit (StemCell technologies). BFP+ Tcells were FACS sorted Genomic DNA (gDNA) from lymphocytes or sorted TMBP cells was isolated with the DNeasy Blood and Tissue Kit (Qiagen). A one-step PCR amplification was performed with Q5 High Fidelity DNA Polymerase by using 2.5µg of gDNA per reaction with Fwd-Lib (mix of 8 staggered primers) and Rev-Lib (consists of 8bp of unique barcode) primers for a total of 24 cycles. Illumina adapters were introduced together with the amplification primers. All primer sequences are listed in Supplementary Table 1. The amplified DNA amplicons were purified with SPRIselect (Beckman Coulter) with a ratio of 1:0.8 (DNA to beads) and eluted in nuclease-free water. The presence of ~250bp DNA amplicons was confirmed and the concentration was measured with Agilent Bioanalyzer on DNA 1000 Chips (5067-1504).

Runs: 1 run, 16.3M spots, 1.2G bases, 669.3Mb

Run	# of Spots	# of Bases	Size	Published
SRR24517654	16,284,695	1.2G	669.3Mb	2023-08-01

ID:: 27723127

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