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Sample GSM6069493 Query DataSets for GSM6069493
Status Public on Sep 28, 2022
Title SNCA TG Input
Sample type SRA
Source name Cortex
Organism Rattus norvegicus
Characteristics tissue: Cortex
condition: Human SNCA transgene
antibody: Input
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 SAMN27914799
SRA SRX15014619

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not applicable for this record

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