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| Status |
Public on Jul 27, 2016 |
| Title |
828M |
| Sample type |
SRA |
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| Source name |
Whole blood
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| Organism |
Canis lupus |
| Characteristics |
Sex: male
age (years): 0.8
social rank: Subordinate
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
RNA purification method: Column
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| 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.
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| Submission date |
Apr 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Rachel A Johnston |
| E-mail(s) |
racheljohnston7@gmail.com
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| Organization name |
Duke University
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| Department |
Evolutionary Anthropology
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| Lab |
Jenny Tung
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| Street address |
130 Science Dr, Rm 108 Biological Sciences
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| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27708 |
| Country |
USA |
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| Platform ID |
GPL21746 |
| Series (1) |
| GSE80440 |
Pervasive effects of aging on gene expression in wild wolves |
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| Relations |
| BioSample |
SAMN04870034 |
| SRA |
SRX1713277 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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