|
| Status |
Public on Mar 07, 2014 |
| Title |
M062209LB |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Sus scrofa |
| Characteristics |
tissue: liver
strain: Yorkshire-Landrace
fed status: Fasted
survival: Lived
time point: Baseline
tissue: liver biopsy
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Liver biopsies were flash frozen with liquid nitrogen and stored until further processing. RNA was extracted using the QIAGEN RNeasy 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 |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava v1.8.2 software used for basecalling.
TopHat v1.5.0 using default settings
BAM files sorted using SAMtools
Raw counts estimated by the Python script HTSeq count
Identified contigs converted to human orthologs with BiomaRt Bioconductor package. HUGO names were used for subsequent analysis
EdgeR v3.2.4 was used with Trimmed mean of M values normalization to calculate differentially expressed genes with respect to time and fed state
Genome_build: Sscrofa10.2.69
Supplementary_files_format_and_content: Supplementary file on Series record with htseq estimated counts of each ensemble gene id, contains all samples by column
|
| |
|
| Submission date |
Mar 06, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Charles Edward Determan Jr |
| Organization name |
University of Minnesota
|
| Department |
Department of Surgery
|
| Lab |
Greg Beilman
|
| Street address |
PWB B150 516 Delware St.
|
| City |
Minneapolis |
| State/province |
MN |
| ZIP/Postal code |
55455 |
| Country |
USA |
| |
|
| Platform ID |
GPL11429 |
| Series (1) |
| GSE55674 |
Fed State Prior to Hemorrhagic Shock and Polytrauma in a Porcine Model Results in Altered Liver Transcriptomic Response |
|
| Relations |
| BioSample |
SAMN02676496 |
| SRA |
SRX482604 |
