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SRX2857412: GSM2640697: A549_Ctrl_IFNg_rep1; Homo sapiens; RNA-Seq
1 ILLUMINA (NextSeq 550) run: 11M spots, 815.9M bases, 341.5Mb downloads

Submitted by: NCBI (GEO)
Study: Cytokine Stimulation of PTPN2-deleted cancer cells
show Abstracthide Abstract
PTPN2 was deleted from a selection of murine and human cancer cells using CRISPR/Cas9. The loss-of-function phenotype was assessed in vitro with cytokine stimulation or vehicle control. Overall design: In order to determine the effect of PTPN2-inhibition of interferon signalling, Cas9-expressing murine (B16 melanoma) and human (A375, A549, HT29, MelJuSo) cancer cells were infected with lentivirus containing guide RNA (sgRNA) against Ptpn2 or a non-targeting sequence. After Ptpn2 deletion was verified, the cell lines were treated with vehicle control (PBS with 0.1% BSA), interferon-beta (IFNb), interferon-gamma (IFNg), or tumor necrosis factor (TNFa), alone or in combination, and transcriptionally profiled by directional, paired-end RNAseq after a 48 hour stimulation.!Series_overall_design = Please note that 'Bro3' and 'Bro4' refer to non-targeting guides provided by the Broad Institute. Please note that 'Bro3' and 'Bro4' refer to non-targeting guides provided by the Broad Institute.
Sample: A549_Ctrl_IFNg_rep1
SAMN07168043 • SRS2228148 • All experiments • All runs
Organism: Homo sapiens
Library:
Instrument: NextSeq 550
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: Cells were trypsinized and lysed in QIAGEN RLT buffer and frozen at -80C. RNA was extracted using QIAGEN Rneasy kits according to manufacturer's instructions. Libraries were constructed using the NEB Ultra-Directional RNA kit using the mRNA capture module, according to manufacturer's instructions. Directional libraries were barcoded using NEB dual index barcodes and sequenced on the NextSeq (high output flowcell) by pair-end sequencing of 37bp.
Experiment attributes:
GEO Accession: GSM2640697
Links:
Runs: 1 run, 11M spots, 815.9M bases, 341.5Mb
Run# of Spots# of BasesSizePublished
SRR560481811,025,000815.9M341.5Mb2017-07-31

ID:
4096607

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