|
| Status |
Public on Jul 10, 2018 |
| Title |
ZDF + Colesevelam - Sample 5 |
| Sample type |
SRA |
| |
|
| Source name |
ZDF + Colesevelam, liver
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: ZDF-Leprfa/Crl
tissue: Liver
age: 8-weeks
phenotype: Obese
agent: Colesevelam
|
| Extracted molecule |
total RNA |
| Extraction protocol |
livers were removed, flash frozen in liquid nitrogen, and RNA was harvested using Norgen Total RNA isolation kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Col_3258_2
|
| Data processing |
All reads ≥16nts in length were aligned to the rat genome (Rnor5.0) by Bowtie1(v1.1.2)[30] allowing one mismatch. DEseq2 (v1.18.1)[31] was used to identify significant (p<0.05) differentially (absolute fold change >1.5) expressed liver miRNAs.
miRNAs that were detected in the sequencing experiment are reported in the processed data file (401 miRNAs). miRNA were considered "detectable" and included in the analysis is 50% of sample had > 5 reads (median 5 reads).
Genome_build: Rnor5.0
Supplementary_files_format_and_content: .csv file includes RPKM values for each Sample
|
| |
|
| Submission date |
Jul 09, 2018 |
| Last update date |
Jul 10, 2018 |
| Contact name |
Leslie Roteta Sedgeman |
| Organization name |
Vanderbilt University
|
| Street address |
2220 Pierce Avenue
|
| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37232 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE116826 |
sRNA sequencing of liver from lean rats and ZDF rats treated with vehicle or colesevelam |
|
| Relations |
| BioSample |
SAMN09633721 |
| SRA |
SRX4370449 |
