|
| Status |
Public on Jun 09, 2023 |
| Title |
TyrRS rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human embryonic kidney
chip antibody: Thermo Fisher Scientific, R960CUS
|
| Treatment protocol |
Cells were grown to 70-80% confluence before treatments.
|
| Growth protocol |
HEK-293 (human embryonic kidney) cells were purchased from ATCC. HEK-293 were grown in DMEM (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Gibco) and penicillin/streptomycin (Gibco). Cultures were maintained at 37°C in a humidified atmosphere under 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with formaldehyde (1% final concentration) for 10 min at room temperature. The reaction was stopped by adding 125 mM glycine. ChIP assays were performed according to the protocol of ChIP-IT Express Enzymatic kit (Active Motif) using ChIP-grade antibody against V5 (Thermo Fisher Scientific, R960CUS), IgG (Cell signaling technology, #5415),
Libraries were prepared and sequenced by the Next Generation Sequencing Core at Scripps Research, La Jolla, California
TF-ChIP-seq
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Reads were quality filtered and adapter trimmed with trimgalore.
ENCODE 3 ChIP-Seq pipeline (ENCODE Project Consortium, 2012) was followed for read mapping and peak calling.
reads were aligned to hg19 with Bowtie2 (Langmead and Salzberg, 2012) and duplicates were removed using picard tools and samtools (Li et al., 2009).
TyrRS binding sites in the genome in comparison to a control input were identified using MACS (Zhang et al., 2008).
Genome_build: hg19
Supplementary_files_format_and_content: peak
|
| |
|
| Submission date |
Jul 28, 2020 |
| Last update date |
Jun 09, 2023 |
| Contact name |
Xiang-Lei Yang |
| E-mail(s) |
xlyang@scripps.edu
|
| Phone |
8587848976
|
| Organization name |
Scripps Research
|
| Department |
Molecular Medicine
|
| Lab |
Yang
|
| Street address |
10550 North Torrey Pines Road BCC-110
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE155309 |
Nuclear translocation of an aminoacyl-tRNA synthetase may mediate a chronic "integrated stress response" |
|
| Relations |
| BioSample |
SAMN15661930 |
| SRA |
SRX8840562 |
