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Sample GSM6281537 Query DataSets for GSM6281537
Status Public on Jun 01, 2024
Title K130
Sample type SRA
 
Source name Kidney
Organism Ictidomys tridecemlineatus
Characteristics tissue: Kidney
hibernation state: SpD
Sex: M
animal number: 130
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 NovaSeq 6000
 
Description Nugen UniversalPlus
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 GPL30340
Series (1)
GSE227101 Kidney gene expression dynamics during torpor-arousal cycles in hibernating 13-lined ground squirrels
Relations
BioSample SAMN29420927
SRA SRX15944567

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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