|
| Status |
Public on Dec 31, 2016 |
| Title |
ChIP_NUP98 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293FT cell line expressing NUP98-FLAG
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293FT cell line expressing NUP98-FLAG
tag: FLAG
cell type: embryonal kidney
chip antibody: Monoclonal ANTI-FLAG® M2 (SIGMA ALDRICH, F3165, lot-SLBG5311 )
|
| Growth protocol |
HEK293FT cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM), supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (Invitrogen)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with the antibody.
Libraries were constructed using the ChIP-seq sample preparation kit (Illumina, San Diego, California, USA)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
Samples were sequenced in a Genome Analyzer IIx (GA2, Illumina) single 40-base read run.
Alignment to the human sequence assembly (GRCh37/hg19, Feb 2009) was performed using BWA with default settings, permitting alignments with 1 mismatch in 40 base reads.
Peak detection was performed using MACS 2.020 following the developer’s technical recommendations (p-value cutoff for peak detection = 10-5). Significant ChIP-seq peaks were established at FDR ≤ 5%.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: wig files with alignments, bed files with peaks provided by MACS
|
| |
|
| Submission date |
Oct 22, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Ana Del Rio |
| E-mail(s) |
[email protected]
|
| Organization name |
CNIO
|
| Street address |
Calle Melchor Fernandez Almagro 3
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL9115 |
| Series (2) |
| GSE62586 |
Evaluation of the NUP98-HOXA9 role as oncogenic transcription factor |
| GSE62587 |
NUP98-HOXA9 role as oncogenic transcription factor |
|
| Relations |
| BioSample |
SAMN03135157 |
| SRA |
SRX738220 |
