GSM1587921: SET2_H3K27ac_untreated_15; Homo sapiens; ChIP-Seq - SRA

SRX849398: GSM1587921: SET2_H3K27ac_untreated_15; Homo sapiens; ChIP-Seq
1 ILLUMINA (Illumina HiSeq 2500) run: 32.7M spots, 1.6G bases, 1.2Gb downloads

Submitted by: Gene Expression Omnibus (GEO)

Study: Effect of cortistatin A (CA) on enhancer occupancy in CA-sensitive and -insensitive human cell lines

PRJNA273301 • SRP052715 • All experiments • All runs

show Abstracthide Abstract

We characterized the marine natural product cortistatin A (CA) as an inhibitor of CDK8 to determine whether pharmacologic inhibition of CDK8 regulates super-enhancer function and inhibits AML proliferation. In this series, we use ChIP-seq of H3K27ac, H3K4me1, MED1, CDK8, BRD4, and RNA polymerase II (PolII) to examine enhancer occupancy and transcriptional response to CA in human cells lines. Overall design: ChIP-seq was carried out in CA-sensitive: MOLM-14 cells (H3K27Ac, H3K4me1, MED1, CDK8, BRD4, and PolII), MV4;11(H3K27Ac, CDK8), SET2 (H3K27Ac, CDK8), and in CA-insensitive cells: K562 (CDK8).

Sample: SET2_H3K27ac_untreated_15

SAMN03290584 • SRS824214 • All experiments • All runs

Organism: Homo sapiens

Library:

Instrument: Illumina HiSeq 2500

Strategy: ChIP-Seq

Source: GENOMIC

Selection: ChIP

Layout: SINGLE

Construction protocol: Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. Libraries for Illumina sequencing were prepared using the Illumina TruSeq ChIP Sample Preparation kit with the following exceptions. After end-repair and A-tailing, ChIP DNA or whole cell extract DNA was ligated to Illumina RNA adaptors with unique indices. Alternatively, libraries were prepared using the KAPA Hyper Prep Kit for Illumina and ligated to unique Bioo Scientific NEXTflex barcode adaptors. Following ligation, libraries were amplified with 16-18 cycles of PCR and were then size-selected using a 2% gel cassette in the Pippin Prep System from Sage Science. For histone modifications and RNA pol II, DNA fragments of size 200-500bp were captured. For CDK8 and MED1, DNA fragments of size 200-450bp were captured. Libraries were quantified by qPCR utilizing the KAPA Biosystems Illumina Library Quantification kit.

Experiment attributes:

GEO Accession: GSM1587921

Links:

External link: GEO Sample GSM1587921

NCBI link: NCBI Entrez (gds)

Runs: 1 run, 32.7M spots, 1.6G bases, 1.2Gb

Run	# of Spots	# of Bases	Size	Published
SRR1768157	32,732,593	1.6G	1.2Gb	2015-10-21

ID:: 1199251

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