|
| Status |
Public on Sep 20, 2018 |
| Title |
id24PregHi En LoPro LCM |
| Sample type |
SRA |
| |
|
| Source name |
Subcutaneous Adipose tissue
|
| Organism |
Bos taurus |
| Characteristics |
time point: Preg
tissue: Subcutaneous Adipose tissue
dietary energy level: Hi
dietary protein level: LoPro
pedigree: LCM
|
| Treatment protocol |
To obtain different growth profiles during rearing, 24 heifers were fed experimental diets differing in energy (Hi/Lo) and protein content (HiPro/LoPro) from 3 mo of age until confirmed successful breeding at 400 kg BW. Thereafter, all heifers were jointly allowed ad libitum access to a low-energy feed during pregnancy. Subcutaneous adipose tissue samples were harvested at 12 mo of age and at 7 months of pregnancy.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from frozen adipose tissue by homogenisation in Trizol and extraction with Qiagen RNeasy lipid tissue mini kits. RNA was then DNAse treated and purified using Turbo DNA-free (Ambion, Life technologies). Standard Illumina paired-end read mRNA-seq libraries were constructed from cDNA which was made from the purified mRNA using Illumina Truseq RNA sample prep kit v2.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Adapter trimming: Cutadapt v1.3, as given in manual for trimming Illumina Truseq adapters
Filtering: Cutadapt v1.3 (settings: -q 25 -m 20)
RNAseq reads were aligned to UMD3.1 genome using Tophat 2.0.12 (settings: --library-type fr-unstranded)
Sorting: Samtools v1.19 (settings: -n)
Counting: HTSEQ-count (settings: -r name -f bam --stranded=no)
Genome_build: UMD3.1.78
Supplementary_files_format_and_content: Tab delimited txt files; First row contains the ENSEMBL gene IDs and second row the raw number of reads that map to each gene
|
| |
|
| Submission date |
Mar 17, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Hilde Kristine Lyby Wærp |
| E-mail(s) |
hilde.lyby@gmail.com
|
| Organization name |
Norwegian University of Life Sciences
|
| Department |
Animal and Aquacultural Sciences
|
| Street address |
Arboretveien 6
|
| City |
Aas |
| ZIP/Postal code |
1432 |
| Country |
Norway |
| |
|
| Platform ID |
GPL15749 |
| Series (1) |
| GSE79347 |
Effects of diets differing in energy and protein content on the adipose tissue transcriptome of Norwegian Red Heifers |
|
| Relations |
| BioSample |
SAMN04565776 |
| SRA |
SRX1639929 |
