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Sample GSM4199232 Query DataSets for GSM4199232
Status Public on Sep 28, 2022
Title Wild-type H3K27ac ChIP-seq
Sample type SRA
 
Source name SH-SY5Y cells
Organism Homo sapiens
Characteristics cell type: SH-SY5Y cells
conditions: Wild-type
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) (https://usegalaxy.org/).
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
E-mail(s) fubo.cheng@med.uni-tuebingen.de
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
Relations
BioSample SAMN13443001
SRA SRX7254951

Supplementary file Size Download File type/resource
GSM4199232_Wild-type_H3K27ac_ChIP-seq.bed.gz 654.1 Kb (ftp)(http) BED
GSM4199232_Wild-type_H3K27ac_ChIP-seq.bigwig 296.6 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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