|
| Status |
Public on Aug 04, 2020 |
| Title |
wild type TFE3 HA rep1 |
| Sample type |
SRA |
| |
|
| Source name |
U5_wild type TFE3 HA
|
| Organism |
Homo sapiens |
| Characteristics |
cell line background: U5
cell type: human neural stem cell line
genotype/variation: wild type TFE3 overexpression
antibody: rabbit anti-HA antibody
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA bound to targeted proteins was extracted as described here: dx.doi.org/10.17504/protocols.io.ufeetje
DNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
genomic DNA isolated using anti-HA antibody in wild type TFE3 (HA tagged)-expressing cells
|
| Data processing |
library strategy: Cut & Run
Sequencing was performed using an Illumina HiSeq 2500 in Rapid Run mode and employed a paired-end, 50 base read length (PE50) sequencing strategy.
Raw reads were aligned to the UCSC hg19 assembly using bowtie2 and peaks were called using SEACR
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include called peaks for each Sample using SEACR.
|
| |
|
| Submission date |
Jan 30, 2020 |
| Last update date |
Aug 12, 2020 |
| Contact name |
Sonali Arora |
| E-mail(s) |
sarora@fredhutch.org
|
| Organization name |
FHCRC
|
| Street address |
1100 Fairview Ave N,
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE137040 |
Comparison of tumor-associated YAP1 fusions identifies a recurrent set of functions critical for oncogenesis |
| GSE144581 |
Comparison of tumor-associated YAP1 fusions identifies a recurrent set of functions critical for oncogenesis [Cut&Run ChIP-seq] |
|
| Relations |
| BioSample |
SAMN13950458 |
| SRA |
SRX7654202 |
