|
| Status |
Public on Mar 13, 2023 |
| Title |
KO REPLICATE 3 (Polysome fraction) |
| Sample type |
SRA |
| |
|
| Source name |
organoids
|
| Organism |
Mus musculus |
| Characteristics |
tissue: primary bladder urothlelial organoids
genotype/variation: ARID1A KO
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Organoid cell lysates were layered only 10-50% sucrose gradient and fractionated. Polysome fraction was collected. 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 |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Library strategy: Polysome-seq
Sequencing was performed using an Illumina HiSeq 2500 in Rapid Run mode and employed a single-end, 50 base read length (SE50) sequencing strategy.
adaptor was trimmed from raw sequencing files, RRNA was removed from sequencing data using bowtie. Files were then aligned to mm10 using STAR2 and counts per gene were generated using HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw values for each Sample.
|
| |
|
| Submission date |
May 11, 2021 |
| Last update date |
Mar 13, 2023 |
| 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 |
GPL17021 |
| Series (2) |
| GSE174283 |
Dissecting the interface between ARID1A and mRNA translation in bladder cancer (Polysome) |
| GSE201222 |
Dissecting the interface between ARID1A and mRNA translation in bladder cancer |
|
| Relations |
| BioSample |
SAMN19110154 |
| SRA |
SRX10861550 |
