|
| Status |
Public on Jun 01, 2024 |
| Title |
K1 |
| Sample type |
SRA |
| |
|
| Source name |
Kidney
|
| Organism |
Ictidomys tridecemlineatus |
| Characteristics |
tissue: Kidney
hibernation state: IBA
Sex: F
animal number: 75
|
| Treatment protocol |
Animals implanted with temperature devices, kidney and adrenal gland tissue collected based on time and body temperature, flash frozen in LN2 immediately after dissection and kept continuously below -70C until RNA extraction.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA extracted by homogenization with polytron in trizol, cleaned up with Direct-zol RNA MiniPrep Kit (Zymo Research)
Libraries were prepared using either the TruSeq Stranded mRNA Library Prep Kit (Illumina) or the Universal Plus mRNA Sequencing Kit (Nugen) as indicated in the sample metadata.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Illumina TruSeq stranded
|
| Data processing |
The raw sequencing reads were first trimmed with cutadapt to remove adaptor sequences, short sequences, and low quality bases (-m17, -q10, 17).
Trimmed reads were mapped to the 13-lined ground squirrel mitochondrial genome with hisat2 and remaining reads were mapped to transcript annotations on the HiC_Itri_2 genome (19) using Salmon (20) with -numBootstraps 50.
These Salmon assignments were imported into R, summarized by gene using tximport, and filtered to retain only genes with rlog-normalized counts of at least seven in at least 4/5 individuals from at least one group.
The counts were then transformed using rlog from the DESeq2 package and processed with limma’s removeBatchEffect to generate count tables corrected for library type.
Assembly: HiC_Itri_2 (https://www.ncbi.nlm.nih.gov/assembly/GCA_004006685.1; DOI: 10.3389/fphys.2020.624677)
Supplementary files format and content: csv file with batch-corrected rlog (log2) count matrix from DESeq2
|
| |
|
| Submission date |
Jun 29, 2022 |
| Last update date |
Jun 01, 2024 |
| Contact name |
Austin E Gillen |
| E-mail(s) |
austin.gillen@cuanschutz.edu
|
| Organization name |
University of Colorado Anschutz Medical Campus
|
| Street address |
12801 East 17th Avenue
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL24271 |
| Series (1) |
| GSE227101 |
Kidney gene expression dynamics during torpor-arousal cycles in hibernating 13-lined ground squirrels |
|
| Relations |
| BioSample |
SAMN29420935 |
| SRA |
SRX15944559 |
