|
| Status |
Public on Aug 04, 2020 |
| Title |
U5_YAP1-MAMLD1 rep3 |
| Sample type |
SRA |
| |
|
| Source name |
U5_YAP1-MAMLD1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U5
cell type: human neural stem cell line
genotype/variation: pLJM1-YAP1-MAMLD1-PGK-Puro
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from cell cultures every two weeks during the exponential growth phase; RNA was isolated from 0.5-1.0×106 cells. Total RNA was prepared using RNeasy Mini Kit with DNase I (Qiagen). RNA concentration and quality (A260/A280) was measured using a NanoDrop 1000 Spectrophotometer (Thermo Scientific)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
U5 neural stem cells transduced with pLJM1-YAP1-MAMLD1-PGK-Puro rep 3
|
| Data processing |
Sequencing was performed using an Illumina HiSeq 2000 in Rapid Run mode and employed a paired-end, 50 base read length (PE50) sequencing strategy.
RNA-seq reads were aligned to the UCSC hg19 assembly using STAR2 and counted for gene associations against the UCSC genes database with HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw values for each Sample.
|
| |
|
| Submission date |
Sep 06, 2019 |
| Last update date |
Aug 06, 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 |
GPL11154 |
| Series (2) |
| GSE137038 |
Comparison of tumor-associated YAP1 fusions identifies a recurrent set of functions critical for oncogenesis[RNASeq] |
| GSE137040 |
Comparison of tumor-associated YAP1 fusions identifies a recurrent set of functions critical for oncogenesis |
|
| Relations |
| BioSample |
SAMN12709279 |
| SRA |
SRX6814130 |
