|
| Status |
Public on Mar 25, 2024 |
| Title |
GLO_n_1_NT_chip_ZEB1 |
| Sample type |
SRA |
| |
|
| Source name |
GLO
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: GLO
treatment: 10% FBS
cell type: Melanoma short-term cultures
antibody: ZEB1
|
| Treatment protocol |
Cells were treated with TNF-α (100 ng/mL) for 14 days, the treatment was replaced every 3 days.
|
| Growth protocol |
Cells were seeded in 15cm dishes and cultivated in RPMI (GLO) or DMEM (AS3) media supplemented with 10% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells from one 15-cm dish were cross-linked with 1% formaldehyde at RT for 10 min and quenched in 125 mM glycine for 5 min. Cross-linked chromatin was isolated and sonicated to generate DNA fragments averaging 200-500 bp in length by Bioruptor plus sonication device (Diagenode). Chromatin fragments were immunoprecipitated with antibodies directed against ZEB1 (1 μg, Genetex, GTX105278), or IgG (1 µg, Bio-Rad, PRABP01) as negative control.
5 ng of input and 30 pg of IP were used. Sequencing was performed with Illumina NovaSeq machine with a paired-end protocol (2x75bp, 64Mp reads).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
IP ZEB1
|
| Data processing |
Raw sequencing reads were processed through nf-core-chipseq-2.0.0 pipeline.
https://github.com/nf-core/chipseq/releases
Assembly: GRCh38
Supplementary files format and content: BigWig files containing normalized coverage for IP samples and pooled control samples.
Supplementary files format and content: BedGraph files containing narrowPeak calling (IP sample vs. pooled control samples).
|
| |
|
| Submission date |
Oct 31, 2023 |
| Last update date |
Mar 25, 2024 |
| Contact name |
Julie CARAMEL |
| E-mail(s) |
[email protected]
|
| Phone |
+33426556705
|
| Organization name |
Cancer Research Center of Lyon
|
| Street address |
28 Rue Laennec
|
| City |
LYON |
| ZIP/Postal code |
69008 |
| Country |
France |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE246672 |
ZEB1 controls a lineage-specific transcriptional program essential for melanoma cell state transitions [ChIP-seq] |
| GSE246673 |
ZEB1 controls a lineage-specific transcriptional program essential for melanoma cell state transitions |
|
| Relations |
| BioSample |
SAMN38052253 |
| SRA |
SRX22321794 |
