GSM3386003: 71_Input; Homo sapiens; ChIP-Seq - SRA

SRX4673571: GSM3386003: 71_Input; Homo sapiens; ChIP-Seq
1 ILLUMINA (NextSeq 500) run: 32.4M spots, 2.4G bases, 997.9Mb downloads

Submitted by: NCBI (GEO)

Study: SWI/SNF component ARID1A restrains pancreatic neoplasia formation [ChIP-seq]

PRJNA490488 • SRP161574 • All experiments • All runs

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ARID1A restrains the formation of PanIN, pancreas ductal adenocarcinoma, and intraductal mucinous neoplasms Overall design: We used immortalized human pancreatic ductal epithelial cells (Ouyang, Am J Path 2000, purchased from ATCC) and used Crispr/Cas9 to generate Arid1a knockout cells. The cells that underwent editing but retained Arid1a expression on Western were used as control. These lines were derived from single cell clones. We performed Chip-Seq against H3K27ac, using input as control. We performed one replicate. Clone 71 was wild-type and clone 9 was knock out.

Sample: 71_Input

SAMN10038473 • SRS3768131 • All experiments • All runs

Organism: Homo sapiens

Library:

Instrument: NextSeq 500

Strategy: ChIP-Seq

Source: GENOMIC

Selection: ChIP

Layout: SINGLE

Construction protocol: Cells were fixed with fresh 1% formaldehyde for 10 min at room temperature and 125 mM glycine was added to inactivate the fixation. Cells were washed by cold PBS 3 times and collected. Cross-linked chromatin was sonicated into fragments of a size range between 250 and 500 nucleotides (Covaris). H3K27Ac antibody (Abcam, ab4729) was incubated with the solubilized DNA fragments at 4°C overnight. Antibody–chromatin complexes were captured by protein A/G Agarose beads (Pierce #20423) and eluted with 1% SDS after extensive washing. The cross-link between DNA and chromatin proteins was reversed by incubation overnight at 65°C. DNA was purified by QIAquick PCR Purification Kit (Qiagen 28104) and dissolved into 30 μL TE buffer per immunoprecipitation. ChIP-seq libraries were generated using KAPA LTP library preparation kit(KK8230) following the manufacturer's protocol (Kapa Biosystems).

Experiment attributes:

GEO Accession: GSM3386003

Links:

NCBI link: NCBI Entrez (gds)

Runs: 1 run, 32.4M spots, 2.4G bases, 997.9Mb

Run	# of Spots	# of Bases	Size	Published
SRR7822404	32,389,241	2.4G	997.9Mb	2018-09-25

ID:: 6332020

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