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| Status |
Public on May 15, 2019 |
| Title |
L32-3 |
| Sample type |
SRA |
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| Source name |
Bovine testes parenchyma
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| Organism |
Bos taurus |
| Characteristics |
diet: Low (12% Crude Protein, 64.4% Total Digestible Nutrients)
age at castration: 32 weeks
tissue: testes
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| Extracted molecule |
total RNA |
| Extraction protocol |
A small portion of testicular parenchyma (~75 mg) from each bull (n=28) was homogenised and total RNA extracted. Trizol reagent-mediated extraction was performed as per manufacturer’s instructions. For each sample (n=28) total RNA (1 µg) was used to create mRNA libraries using the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Base calling and demultiplexing were done with CASAVA 1.9 (Illumina) with default settings. Initial quality control, conducted with FastQC detected no adapter sequences, base qualities and other parameters were excellent.
Sequenced reads were aligned to the bovine genome (Bos taurus, UMD3.1.87, downloaded from Illumina iGENOME website) using TopHat, with Bowtie2 as an internal aligner.
FeatureCounts program was used to count number of reads on each exon by transcript meta-feature
To conduct a “per-gene” analysis, the most expressed transcript over all conditions was selected by the provided ad hoc python script (select_protein_coding_transcripts.py).
Count-tables obtained with FeatureCounts was loaded, and the count in each sample normalised by library size. Normalised counts on protein coding genes were used for analysis of differential expression with DESeq2 in R package (version 1.14.1) via SARTools6 (Version 1.4.0) package
Genome_build: Bos taurus, UMD3.1.87
Supplementary_files_format_and_content: rawcounts contain raw counts of reads mapping to features.
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| Submission date |
Jan 14, 2019 |
| Last update date |
May 15, 2019 |
| Contact name |
Chinju Therese Johnson |
| E-mail(s) |
chinju.johnson@ucalgary.ca
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| Phone |
5879696326
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| Organization name |
University of Calgary
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| Department |
Production Animal Health
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| Lab |
Theriogenology
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| Street address |
8824 46 Ave. N.W.
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| City |
Calgary |
| State/province |
Alberta |
| ZIP/Postal code |
T3B1Y8 |
| Country |
Canada |
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| Platform ID |
GPL23055 |
| Series (1) |
| GSE125082 |
Enhanced early-life nutrition upregulates cholesterol biosynthetic gene expression and Sertoli cell maturation in testes of pre-pubertal Holstein bulls |
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| Relations |
| BioSample |
SAMN10742260 |
| SRA |
SRX5248985 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3562389_L32-3_rawcount.txt.gz |
1.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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