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Sample GSM5290994 Query DataSets for GSM5290994
Status Public on Mar 13, 2023
Title KO REPLICATE 3 (Subpolysome 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. Subpolysome 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 SAMN19110132
SRA SRX10861548

Supplementary file Size Download File type/resource
GSM5290994_SJ22_G38_S12.hts.txt.gz 96.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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