|
| Status |
Public on Sep 28, 2022 |
| Title |
Wild-type Rabbit IgG control |
| Sample type |
SRA |
| |
|
| Source name |
SH-SY5Y cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: SH-SY5Y cells
conditions: Wild-type
antibody: anti-rabbit IgG (Cell signaling, 2729)
|
| 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 |
SAMN13442999 |
| SRA |
SRX7254953 |
