|
| Status |
Public on Jul 14, 2021 |
| Title |
911 Hypothalamus |
| Sample type |
SRA |
| |
|
| Source name |
Hypothalamus
|
| Organism |
Bos taurus |
| Characteristics |
diet: Moderate
tissue: Hypothalamus
breed: Holstein-Friesian X Angus
|
| Treatment protocol |
Calves on the High-plane of nutrition received 1.5 kg of milk replacer (10 liters) per day and ad libitum concentrates during the calf phase. During the subsequent post-weaning phase this group were then offered concentrates ad libitum and hay to appetite. During the calf phase the Moderate plane of nutrition group received 0.5 kg of milk replacer (4 litres) per day and 1 kg of concentrates, subsequently receiving 1kg of concentrates and hay to appetite during the post-weaning phase. The calf phase lasted for 8 weeks and was followed by the post-weaning phase which lasted for 11 weeks.
|
| Growth protocol |
Angus X Holstein-Friesian heifer calves were fed differentially either a High plane of nutrition (n=14) or a Moderate plane of nutrition (n=15) from 2-21 weeks of age. Calves on the High plane of nutrition were expected to grow at 1.2 kg/day, with the Moderate plane of nutrition expected to gain 0.5 kg/day.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was precipitated and purified from hypothalamus samples using the Qiagen RNeasy Plus Universal kit (Qiagen, UK) 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 Illumina TruSeq stranded RNA sample prep kit (Illumina, San Diego, CA, USA), following the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Moderate-plane of nutrition
Hypothalamus_merged_counts.txt
|
| 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.
A false discovery rate (FDR) of <0.1 was applied as a threshold to call genes with differential expression levels.
Genome_build: UMD 3.1
Supplementary_files_format_and_content: Tab delimited txt file of merged gene read counts
|
| |
|
| Submission date |
Jun 29, 2020 |
| Last update date |
Jul 14, 2021 |
| 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) |
| GSE153495 |
Effect of early-life plane of nutrition on the transcriptional profile of the hypothalamus in heifer calves |
|
| Relations |
| BioSample |
SAMN15399266 |
| SRA |
SRX8632747 |
