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Sample GSM6069499 Query DataSets for GSM6069499
Status Public on Sep 28, 2022
Title SNCA TG-L Cortex H3K4me3
Sample type SRA
Source name Cortex
Organism Rattus norvegicus
Characteristics tissue: Cortex
condition: Human SNCA transgene low level
antibody: anti-H3K4me3 (Cell signaling, C42D8)
Extracted molecule genomic DNA
Extraction protocol Brain tissues 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 NovaSeq 6000
Data processing Base calling performed using Illumina bcl2fastq2 version 2.19.1
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 bamcoverage bigwig files were generated using aligned bam files
Assembly: hg19
Supplementary files format and content: bigwig coverage files
Submission date Apr 27, 2022
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 GPL25947
Series (2)
GSE141278 Transcription regulation of SNCA by dystonia type 6 gene product THAP1
GSE201686 Transcription regulation of SNCA by dystonia type 6 gene product THAP1 [Rat_ChIP-seq]
BioSample SAMN27914793
SRA SRX15014625

Supplementary file Size Download File type/resource
GSM6069499_SNCA_TG-L_Cortex_H3K4me3.bigwig 8.2 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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