|
| Status |
Public on Dec 16, 2015 |
| Title |
NRF1_INPUT_HCC1954 |
| Sample type |
SRA |
| |
|
| Source name |
breast cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCC1956
genotype: WT
chip antibody: none (input)
|
| Growth protocol |
HCC1954 cells were cultured in RPMI 1640 medium supplemented with 10% fetal calf serum, 1× nonessential amino acids and 1× L-glutamine (37°C, 5% CO2).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitation (ChIP) was carried out essentially as previously described (Jermann et al. PNAS 2014).
Library Construction Protocol: Libraries for ChIP-seq were prepared according to standard Illumina library preparation protocols. Twelve cycles of PCR (NEB Q5 Hot Start HiFi PCR) were performed on end-repaired, A-tailed and adapter-ligated DNA prior to gel size-selection. Quality of the libraries and size distribution was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies). Sequencing was performed on an Illumina HiSeq 2500 machine (50 bp read length, single end) according to Illumina standards.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalling was performed with the Illumina RTA 1.17.21.3 software with default parameters
Fastq files were generated with the Illumina bcl2fastq-1.8.4 software with options --use-bases-mask Y50n,I6n --fastq-cluster-count 100000000 --no-eamss
Read mapping was performed using Bowtie version 1.0.0 with parameters -v 3 -m 1 --best --strata.
Bigwig files were generated by extending the reads to 200bp and calculating for each genomic position the read density normalized to one million reads in the library.
Genome_build: hg19
|
| |
|
| Submission date |
Sep 23, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Anais Flore Bardet |
| Organization name |
IGBMC
|
| Street address |
1 rue Laurent Fries
|
| City |
Illkirch |
| ZIP/Postal code |
67404 |
| Country |
France |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE67867 |
Competition between DNA methylation and transcription factors determines binding of NRF1 |
|
| Relations |
| BioSample |
SAMN04103867 |
| SRA |
SRX1280453 |
