|
| Status |
Public on Mar 15, 2019 |
| Title |
R1ko rep2 |
| Sample type |
SRA |
| |
|
| Source name |
colon
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Tnfrsf1a-/-
strain: C57Bl/6J
tissue: colon
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Extraction protocol was the standard protocol associated with the PureLink RNA Mini Kit (ThermoFisher Scientific). Library construction protocol was the paired-end protocol in the SMARTer Universal Low Input RNA Kit for Sequencing (Clontech).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed_tpm.csv
|
| Data processing |
pseudoalignment and transcript quantification with kallisto 0.43.1
statistical significance calling with sleuth
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated text file with tpm calculations for each annotated transcript for each sample
|
| |
|
| Submission date |
Dec 11, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Cambrian Yangshao Liu |
| E-mail(s) |
cambrian@uchicago.edu
|
| Organization name |
The University of Chicago
|
| Department |
Department of Medicine
|
| Street address |
5841 S Maryland Ave
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE107933 |
Transcriptome analysis of TNFR1-knockout mouse colon |
|
| Relations |
| BioSample |
SAMN08166010 |
| SRA |
SRX3465270 |
