|
| Status |
Public on Apr 22, 2020 |
| Title |
WT-140 |
| 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 |
| E-mail(s) |
leipinji@gmail.com
|
| 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 |
|
| Relations |
| BioSample |
SAMN12672692 |
| SRA |
SRX6790158 |
