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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
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 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]
Relations
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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