|
| Status |
Public on Jan 01, 2014 |
| Title |
Short Day - rep 7 |
| Sample type |
SRA |
| |
|
| Source name |
Subcutaneous adipose
|
| Organism |
Felis catus |
| Characteristics |
treatment: Short Day
tissue: Subcutaneous adipose
individual: Monster
day length: Short
presentation order: P1
|
| Treatment protocol |
During two 12-wk periods, cats were exposed to either short days (8 hr light:16 hr dark) or long days (16 hr light:8 hr dark). Subcutaneous adipose biopsies were collected at wk 12 of each period for RNA isolation and Illumina sequencing.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Subcutaneous adipose samples were removed, flash frozen in liquid nitrogen, and total RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries. Indices (barcodes) were included to be able to differentiate the sequences from each sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The libraries were quantitated by qPCR, pooled all together and sequenced on three lanes for 101 cycles on a HiSeq 2000 using a TruSeq SBS sequencing kit version 3
Base calling and de-multiplexing of samples within each lane were done with Casava 1.8.2. Reads from the same sample across multiple lanes were combined into one .fastq.gz file using an in-house pipeline.
Reads were trimmed for quality using seqtk (downloaded 12/2012 from github.com/lh3/seqtk) with parameters trimfq -q 20 -l 25 .
Alignments to the cat genome (Felis_catus_6.2) and cat transcriptome (Ensembl 70) were done using Tophat2 2.0.8 with parameters --b2-very-sensitive --no-sort-bam --transcriptome-index transcriptome/known. Sorting of the BAM files was done with novosort (novocraft 2.08.02) with parameters -f -c.
Read counts for each gene were generated using htseq-count (samtools 0.1.18) with parameters --stranded=no -m intersection-nonempty and combined into one tab-delimited text file for all 20 samples
Genome_build: Felis_catus_6.2
Supplementary_files_format_and_content: a single tab-delimited text file of raw read counts were used directly in edgeR 3.0.8 for statistical analysis and thus are the "normalized" data.
|
| |
|
| Submission date |
Apr 26, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Kelly Scott Swanson |
| E-mail(s) |
ksswanso@uiuc.edu
|
| Organization name |
University of Illinois
|
| Street address |
1207 W. Gregory Dr.
|
| City |
Urbana |
| State/province |
IL |
| ZIP/Postal code |
61801 |
| Country |
USA |
| |
|
| Platform ID |
GPL17081 |
| Series (1) |
| GSE46431 |
Effect of photoperiod on feline adipose transcriptome profiles as assessed by RNA sequencing |
|
| Relations |
| BioSample |
SAMN02058450 |
| SRA |
SRX272142 |
