|
| Status |
Public on Dec 01, 2017 |
| Title |
ATF3_WT_24h |
| Sample type |
SRA |
| |
|
| Source name |
CS1AN+CSBwt
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: dermal fibroblasts, immortolized
treatments: UV-C, 12 J/m2
chip antibody: ATF3 (Santa Cruz, sc-188x)
|
| Treatment protocol |
UV-C, 12 J/m2
|
| Growth protocol |
DMEM/HamF10 (1:1) + 10 % FCS and 40 mg/ml gentamycin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and DNA-containing complexes were isolated with antibody.
Diagenode MicroPlex Library Preparation kit v2
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome hg19 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Peaks were called by Macs1.4.2 and were annotated by Homer v4.8 and with Ensembl release 75
Genome_build: hg19
Supplementary_files_format_and_content: Excel table with macs1 peak calling result and Ensembl 75 gene annotations
|
| |
|
| Submission date |
Oct 03, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Tao YE |
| Organization name |
IGBMC (CNRS/INSERM/UDS)
|
| Street address |
1 rue Laurent Fries
|
| City |
Illkirch |
| ZIP/Postal code |
67404 |
| Country |
France |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE87562 |
Cockayne syndrome A and B proteins regulate the transcription arrest upon genotoxic stress through a ubiquitin/proteasome degradation process (ChIP-seq) |
| GSE87564 |
Cockayne syndrome A and B proteins regulate the transcription arrest upon genotoxic stress through a ubiquitin/proteasome degradation process |
|
| Relations |
| BioSample |
SAMN05859553 |
| SRA |
SRX2207917 |
