|
| Status |
Public on May 10, 2021 |
| Title |
L11 (SpD-2) |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Ictidomys tridecemlineatus |
| Characteristics |
hibernation state: SpD
animal number: 80
Sex: F
tissue: liver
|
| Treatment protocol |
animals implanted with temperature devices, liver tissue collected based on time and body temperature, flash frozen in N2l immediately after dissection and kept continuously below -70oC 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)
Strand-specific RNA-seq libraries (TruSeq Stranded mRNA Library Prep Kit, Illumina, constructed at Genewiz)
|
| |
|
| Library strategy |
ssRNA-seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
SpD-2
|
| Data processing |
received off sequencer de-multiplexed files from Genewiz
cutadapt with options -m17 -q10 -a AGATCGGAAGAGC -A AGATCGGAAGAGC (these are the submitted fastq files)
aligned to I. tridecemlinatus mtDNA (hisat2, option --no-spliced-alignment), those that did not align were then aligned to the HiC_Itri_2 genome for gene based quantification using Salmon
salmon assignments were summarized by gene using tximport and normalized using DESeq2's rlog function.
normalized gene-level counts were then filtered to retain only genes with rlog ≥ 7 in at least 4/5 individuals from at least one physiological group
Genome_build: 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 rlog (log2) count matrix from DESeq2
|
| |
|
| Submission date |
Feb 16, 2021 |
| Last update date |
May 10, 2021 |
| Contact name |
Sandy Martin |
| E-mail(s) |
sandy.martin@cuanschutz.edu
|
| Organization name |
University of Colorado School of Medicine
|
| Department |
Cell and Developmental Biology
|
| Street address |
12801 E. 17th Ave.
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL24271 |
| Series (1) |
| GSE166814 |
Liver transcriptome dynamics during hibernation are shaped by a shifting balance between transcription and RNA stability |
|
| Relations |
| BioSample |
SAMN17923096 |
| SRA |
SRX10107484 |
