|
| Status |
Public on May 15, 2024 |
| Title |
UOK120 cells - second TFE3 chip |
| Sample type |
SRA |
| |
|
| Source name |
renal carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: renal carcinoma
cell line: UOK120 cell line
genotype: TFE3 antibody
|
| Growth protocol |
Cells were cultured in DMEM supplemented with 10% FBS (Gibco) and 1% penicillin/streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were cultured and subsequently crosslinked in 1% formaldehyde and processed according to the protocol from the Pierce™ Agarose ChIP Kit. ChIP was performed in UOK109and UOK120 cells using the TFE3 antibody. Immunoprecipitated genomic DNA was used for sequencing analysis.
The purified DNA fragments were end-repaired, tail-added and joined to construct sequenced libraries.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
UOK120 CHIP
|
| Data processing |
ChIP-seq data were obtained using an Illumina Hiseq 2000 sequencerand sequencing reads were de-multiplexed by Illumina pipeline.
ChIP-seq data were mapped to the human genome (hg19) using Bowtie algorithm with up to 2 mismatch allowed and reads mapping to more than 20 locations along the genome were discard.
ChIP-seq data generated form IgG were used against the sample data in calling enriched regions and to control for false discovery rate (FDR).
Peaks were called using MACS version 2, with q-value to 0.05.
Assembly: hg19
|
| |
|
| Submission date |
May 10, 2024 |
| Last update date |
May 15, 2024 |
| Contact name |
Yi Chen |
| E-mail(s) |
DG20350032@smail.nju.edu.cn
|
| Phone |
13914747824
|
| Organization name |
Nanjing Unversity
|
| Department |
Medical school
|
| Street address |
22 Hankou Road
|
| City |
Nanjing |
| ZIP/Postal code |
210000 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE267212 |
TFE3 fusions escape from controlling of mTOR signaling pathway and accumulate in the nucleus promoting genes expression in Xp11.2 translocation renal cell carcinomas. |
|
| Relations |
| BioSample |
SAMN41328382 |
| SRA |
SRX24523147 |
