GSM6139244: mouse HGG, Sox9-GOF, Input, rep2; Mus musculus; ChIP-Seq - SRA

SRX15259347: GSM6139244: mouse HGG, Sox9-GOF, Input, rep2; Mus musculus; ChIP-Seq
1 ILLUMINA (NextSeq 550) run: 74.2M spots, 10.2G bases, 4.3Gb downloads

External Id: GSM6139244_r1

Submitted by: Baylor College of Medicine

Study: Sox9 directs divergent epigenomic states in brain tumor subtypes (ChIP-Seq)

PRJNA837888 • SRP375107 • All experiments • All runs

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The goal of this study was to profile active H3K27ac marks between autochthonous mouse models of high-grade glioma (HGG) and ependymoma (EPN). Furthermore, with the objective of how transcription factor Sox9 affect H3K27ac states in these two models, we also profiled H3K27ac status between HGG and EPN after Sox9 overexpression (Sox9-GOF) or deletion (Sox9-LOF) in each of these models. In addition, we extended our studies to evaluate both H3K27ac and Sox9 states in human HGG and mouse EPN derived tumor cells. Overall design: Chromatin immunoprecipitation (ChIP-seq) for H3K27ac in tumors from mouse models HGG, EPN and human HGG; ChIP-Seq for Sox9 in human HGG; ChIP-Seq for Sox9 from mouse EPN derived tumor cells. All experiments performed in independent biological replicates except for human HGG and mouse EPN derived cells.

Sample: mouse HGG, Sox9-GOF, Input, rep2

SAMN28233646 • SRS12988888 • All experiments • All runs

Organism: Mus musculus

Library:

Name: GSM6139244

Instrument: NextSeq 550

Strategy: ChIP-Seq

Source: GENOMIC

Selection: ChIP

Layout: SINGLE

Construction protocol: Tissue was dissociated, crosslinked with 1.1% formaldehyde for 10 min, quenched and frozen. After thawing, cells were lysed to release nuclei, followed by nuclear lysis. Lysates were sonicated using a Diagenode Bioruptor. ChIP-Seq libraries were prepared using the TruSeq ChIP Library Preparation Kit (Ilumina, IP-202-1012). 10 ng of DNA was used as starting material for Input and IP samples. Libraries ranging from 250-350 bp were extracted from agarose gel incisions and PCR amplified for 18 cycles. Libraries were purified using AMPure XP beads and library quality was validated using a Standard Sensitivity NGS Fragment Analysis Kit.

Runs: 1 run, 74.2M spots, 10.2G bases, 4.3Gb

Run	# of Spots	# of Bases	Size	Published
SRR19194552	74,156,517	10.2G	4.3Gb	2022-05-20

ID:: 21786968

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