|
Status |
Public on Sep 28, 2022 |
Title |
SNCA TG-L Input |
Sample type |
SRA |
|
|
Source name |
Cortex
|
Organism |
Rattus norvegicus |
Characteristics |
tissue: Cortex condition: Human SNCA transgene low level 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 |
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 |
SAMN27914798 |
SRA |
SRX15014620 |