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Sample GSM2127386 Query DataSets for GSM2127386
Status Public on Jul 27, 2016
Title 712M
Sample type SRA
 
Source name Whole blood
Organism Canis lupus
Characteristics Sex: male
age (years): 6
social rank: Alpha
Extracted molecule total RNA
Extraction protocol Whole blood was preserved in PAXgeneTM Blood RNA tubes. Total RNA was extracted using the PAXgene Blood RNA kit.Total RNA was treated with the Globin-Zero kit and purified with the Qiagen RNeasy MinElute® column cleanup procedure or ethanol precipitation (listed in description column).
cDNA libraries were synthesized using a strand-specific kit from Epicentre (ScriptSeqTM v2 Library Prep kit, Illumina) with ScriptSeq Indexes PCR primers.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description RNA purification method: EtOH precip.
Data processing Reads were filtered with Trim Galore v.0.3.1 with the following parameters: --q 20 --l 25 --s 3
Reads were mapped to the Canis lups familiaris genome (Ensembl CanFam3.1.74, unmasked) using Tophat2 v.2.0.10. We allowed up to 3 mismatches, a total of 3 bp length of gaps, and an edit distance no more than 3 bp between the reads and the ref sequence.
The expression level of each gene was quantified using the union mode of the python script htseq-count (HTSeq 0.6.1)
Genes were filtered to only include protein-coding genes with at least 10 reads in at least 75% of cDNA libraries (N = 13,558 protein-coding genes).
We used conditional quantile normalization (cqn package in R) to normalize for sequencing depth (TMM), GC-content, and gene length (averaged from the transcripts in the canFam3.1.74 gtf file).
Supplementary_files_format_and_content: Tab-delimited text file containing gene transcript abundance measurements. The unit of measure is the log2 transformed read counts controlling for library size, GC content, and gene length, as produced by CQN (R package) and analagous to RPKM.
 
Submission date Apr 19, 2016
Last update date May 15, 2019
Contact name Rachel A Johnston
E-mail(s) racheljohnston7@gmail.com
Organization name Duke University
Department Evolutionary Anthropology
Lab Jenny Tung
Street address 130 Science Dr, Rm 108 Biological Sciences
City Durham
State/province NC
ZIP/Postal code 27708
Country USA
 
Platform ID GPL21746
Series (1)
GSE80440 Pervasive effects of aging on gene expression in wild wolves
Relations
BioSample SAMN04870019
SRA SRX1713262

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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