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Sample GSM4056800 Query DataSets for GSM4056800
Status Public on Apr 22, 2020
Title WT-139
Sample type SRA
Source name Colon
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: colon
treatment: 2.5% DSS treated for 5 days followed by two-day normal water
age: 8 weeks
genotype: Usp25+/+
Extracted molecule polyA RNA
Extraction protocol Colons (0.5 cm in length, 0.5-1cm away from the anus) were removed, split open, washed with PBS, immersed and homogeneized in 2 ml TRIzol, and toral RNA was harvested. Oligo dT was used to purify poly(A) mRNA which was subsequently reverse-transcibed into cDNA for libary construction and Illumina TruSeq.
RNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
Data processing Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
Submission date Sep 02, 2019
Last update date Apr 22, 2020
Contact name Pin-Ji Lei
Organization name Massachusetts General Hospital
Department Department of Radiation Oncology
Lab Edwin L. Steele Laboratories
Street address 100 Blossom Street
City Boston
State/province Massachusetts
ZIP/Postal code 02114
Country USA
Platform ID GPL21273
Series (1)
GSE136727 mRNA transcriptome sequencing of colon tissues from Usp25+/+ and Usp25-/- mice treated with 2.5% DSS for 5 five days followed by two-day normal water
BioSample SAMN12672693
SRA SRX6790157

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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