|
Status |
Public on Aug 04, 2020 |
Title |
YAP1-TFE3 rep1 |
Sample type |
SRA |
|
|
Source name |
whole tumor tissue RCAS-YAP1-TFE3
|
Organism |
Mus musculus |
Characteristics |
tissue: mouse brain tumor genotype/variation: RCAS-YAP1-TFE3
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was extracted from cell cultures every two weeks during the exponential growth phase; RNA was isolated from 0.5-1.0×10^6 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 |
XYT7_1
|
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 mm10 assembly using STAR2 and counted for gene associations against the UCSC genes database with HTSeq Genome_build: mm10 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 |
GPL13112 |
Series (2) |
GSE137039 |
Comparison of tumor-associated YAP1 fusions identifies a recurrent set of functions critical for oncogenesis [mouse RNA-seq] |
GSE137040 |
Comparison of tumor-associated YAP1 fusions identifies a recurrent set of functions critical for oncogenesis |
|
Relations |
BioSample |
SAMN12709257 |
SRA |
SRX6814152 |