GSM5602451: SHSY5Y THAP1 ChIP-seq Rep2; Homo sapiens; ChIP-Seq - SRA

SRX12391709: GSM5602451: SHSY5Y THAP1 ChIP-seq Rep2; Homo sapiens; ChIP-Seq
1 ILLUMINA (Illumina NovaSeq 6000) run: 41.4M spots, 4.2G bases, 1.2Gb downloads

External Id: GSM5602451_r1

Submitted by: Institute of Medical Genetics and Applied Genomics, University of Tuebingen

Study: THAP1 is cell type dependent regulator of SP1 family crucial for dystonic syndromes in human and rat [SHSY5Y_ChIP-seq]

PRJNA767100 • SRP339182 • All experiments • All runs

show Abstracthide Abstract

THAP1 is a transcription factor and its mutations are responsible for DYT6 dystonia. However, how THAP1 mutations lead to these gene expression alterations and whether the gene expression changes are also reflected in the brain of THAP1 patients are still unclear. In this study we used epigenetic and transcriptomic approaches combined with multiple model systems to uncover the function of THAP1 and the potential pathogenesis of DYT6 dystonia. THAP1 mutations lead to dysregulation of genes mainly through regulation of SP1 family members, SP1 and SP4, in a cell type dependent manner. Overall design: ChIP-seq analysis of wild-type and THAP1 heterozygous knock-out SHSY5Y cells

Sample: SHSY5Y THAP1 ChIP-seq Rep2

SAMN21889457 • SRS10361612 • All experiments • All runs

Organism: Homo sapiens

Library:

Name: GSM5602451

Instrument: Illumina NovaSeq 6000

Strategy: ChIP-Seq

Source: GENOMIC

Selection: ChIP

Layout: SINGLE

Construction protocol: Cells were crosslinked by 1% formaldehyde (ThermoFisher scientific) and sonicated in RIPA buffer (10 mM Tris-HCl, 1 mM EDTA, 0.5% sodium deoxycholate, 0.1% SDS, 1% NP-40, 1× Protease inhibitor cocktail (Roche), pH 8.0) to 200-500 bp. The sonicated lysate was subjected to immunoprecipitation with specific antibody. The immunoprecipitated DNA (at least 1ng) was purified and subjected to libraries generation. ChIP-seq libraries were generated using NEBNext® Ultra™ II DNA Library Prep Kit (New England Biolabs) according to the manufacturer's instructions.

Runs: 1 run, 41.4M spots, 4.2G bases, 1.2Gb

Run	# of Spots	# of Bases	Size	Published
SRR16106128	41,355,080	4.2G	1.2Gb	2022-09-28

ID:: 16702926

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