|
| Status |
Public on Sep 13, 2022 |
| Title |
L5 |
| Sample type |
SRA |
| |
|
| Source name |
Spermatozoa
|
| Organism |
Bos taurus |
| Characteristics |
fertility status: Low fertility
tissue: Spermatozoa
breed: Holstein-Friesian
|
| Treatment protocol |
High and Low fertility bulls were selected using an animal adjusted statistical model
|
| Growth protocol |
Frozen-thawed semen from Holstein Friesian bulls
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was precipitated and purified from spermatozoa using trizol according to the manufacturer’s guidelines, which included a step to remove any contaminating genomic DNA.
cDNA libraries were prepared from high quality RNA using the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina (NEB, Ipswich, MA, USA), following the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Low fertility
|
| Data processing |
FASTQC software (v0.11.8) was used to check the quality of the raw sequencing reads.
Sequencing indexing adapters were removed using Cutadapt (v2.6)
Input reads were then aligned to the bovine reference genome (UMD3.1) using STAR (v2.6.1), incorporating the quantmode function to determine the number of mapped reads.
The R (v3.4) Bioconductor package, EdgeR (v3.5), was applied to identify statistically significant differentially expressed genes.
Genome_build: ARS1.2
Supplementary_files_format_and_content: Tab delimited txt file of merged gene read counts
|
| |
|
| Submission date |
Mar 07, 2022 |
| Last update date |
Sep 13, 2022 |
| Contact name |
Kate Keogh |
| Organization name |
Teagasc Grange
|
| Department |
Animal and Bioscience Department
|
| Street address |
Dunsany
|
| City |
Co. Meath |
| ZIP/Postal code |
0000 |
| Country |
Ireland |
| |
|
| Platform ID |
GPL26012 |
| Series (1) |
| GSE198043 |
Effect of divergence in fertility on mRNA profling in spermatozoa of bulls |
|
| Relations |
| BioSample |
SAMN26506680 |
| SRA |
SRX14396912 |
