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Sample GSM4199233 Query DataSets for GSM4199233
Status Public on Sep 28, 2022
Title THAP1 KD H3K27ac ChIP-seq
Sample type SRA
Source name SH-SY5Y cells
Organism Homo sapiens
Characteristics cell type: SH-SY5Y cells
conditions: THAP1 knock-down
antibody: anti-H3K27ac (Cell signaling, D5E4)
Growth protocol SH-SY5Y cells were cultured in DMEM medium with 10% FBS and 1% Glutmax at 37℃ in a humidified atmosphere containing 5% CO2.
Extracted molecule genomic DNA
Extraction 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.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
Data processing Base calling performed using Illumina bcl2fastq2 version 2.19.1
ChIP-seq data analysis was performed in Galaxy platform (Galaxy Version 1.2.0) (
ChIP-seq raw reads were aligned to the hg19 genome assembly using Bowtie. Only reads that uniquely mapped to the genome were used for further analysis.
ChIP-seq peaks were identified using MACS.
Genome_build: hg19
Supplementary_files_format_and_content: bed files with all peaks information
Submission date Dec 02, 2019
Last update date Sep 28, 2022
Contact name Fubo Cheng
Organization name University of Tuebingen
Department Institute of Medical Genetics and Applied Genomics
Street address Calwerstrasse 7
City Tuebingen
ZIP/Postal code 72076
Country Germany
Platform ID GPL18573
Series (2)
GSE141244 Transcription regulation of SNCA by dystonia type 6 gene product THAP1 [ChIP-seq]
GSE141278 Transcription regulation of SNCA by dystonia type 6 gene product THAP1
BioSample SAMN13443000
SRA SRX7254952

Supplementary file Size Download File type/resource
GSM4199233_THAP1_KD_H3K27ac_ChIP-seq.bed.gz 643.2 Kb (ftp)(http) BED
GSM4199233_THAP1_KD_H3K27ac_ChIP-seq.bigwig 333.6 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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