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SRX21218111: GSM7673592: sgIkzf1_Tpex_3; Mus musculus; ATAC-seq
1 ILLUMINA (Illumina HiSeq 4000) run: 140.8M spots, 14.4G bases, 4.4Gb downloads

External Id: GSM7673592_r1
Submitted by: Immunology, St Jude Children's Research Hospital
Study: Single-cell CRISPR screens in vivo map T cell fate regulomes in cancer [Ikzf1 ATAC-Seq]
show Abstracthide Abstract
The gene regulatory network (GRN) underlying CTL differentiation and whether Tex responses can be functionally reinvigorated are incompletely understood. Here, we systematically mapped causal GRNs via single-cell CRISPR (scCRISPR) screens in vivo and discovered checkpoints for CTL differentiation. Overall design: We used ATAC seq to compare chromatin accessibility profiles of Ikzf1 KO and Spike Tpex and Tex OT-I T cells from the dual-color transfer system at day 7 post adoptive transfer to B16-OVA tumor
Sample: sgIkzf1_Tpex_3
SAMN36794185 • SRS18475386 • All experiments • All runs
Organism: Mus musculus
Library:
Name: GSM7673592
Instrument: Illumina HiSeq 4000
Strategy: ATAC-seq
Source: GENOMIC
Selection: other
Layout: PAIRED
Construction protocol: Cells were lysed in 50μl ATAC-seq lysis buffer (10mM Tris-HCl, pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630 detergent) on ice for 10min. Resulting nuclei were pelleted at 500gfor 10min at 4 °C. Supernatant was carefully removed with a pipette and discarded. The pellet was resuspended in 50μl transposase reaction mix (25μl 2×TD buffer, 22.5μl nuclease-free water, 2.5μl transposase) and incubated for 30min at 37 °C. After the reaction, the DNA was cleaned up using the Qiagen MinElute kit The barcoding reaction was run using the NEBNext HiFi kit on the basis of the manufacturer's instructions and amplified for five cycles
Runs: 1 run, 140.8M spots, 14.4G bases, 4.4Gb
Run# of Spots# of BasesSizePublished
SRR25486512140,792,57814.4G4.4Gb2023-10-27

ID:
28654607

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