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| Status |
Public on Jun 09, 2021 |
| Title |
Transcriptome profiling of two purebred cattle and their crossbreds |
| Organism |
Bos taurus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: The aim of this study is to determine the absolute and relative expresson levels of mRNA transcripts across two purbred (Angus and Brahman) cattle and their receipicalcross.
Methods: Total RNA was extracted and purified from five tissues using the RiboZero Gold kit. Sequencing libraries were prepared with a KAPA Stranded RNA-Seq Library Preparation Kit following the Illumina paired-end library preparation protocol. Completed libraries were sequenced on HiSeq 2000 as 100 bp paired-end reads at the Australian Cancer Research Foundation (ACRF) Cancer Genomics Facility, Adelaide, Australia and USDA-ARS-US Meat Animal Research Center, Clay Center, USA. Approximately 60 million 100 bp single-end reads were obtained for each sample. Reads were aligned to the cattle reference genome UOA_brahman_1/UOA_angus_1 and mapped to known genomic features at the gene level using the Hisat2. Single reads were then summarized into gene-level counts using FeatureCounts.
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| Overall design |
We used animals and semen of Angus (Bos taurus taurus) and Brahman (Bos taurus indicus) cattle, subsequently referred as Bt and Bi respectively. Pure Bt and Bi females of approximately 16-20 months of age were maintained on pasture supplemented with silage. Fetuses produced by artificial insemination with semen of pure bred Bt or Bi sires. Cows were pregnancy tested by ultrasound scanning. Cows and fetuses were humanely sacrificed by stunning and exsanguination at day 153+/- 1 of gestation. Fetuses were dissected, tissues snap-frozen in liquid nitrogen and stored at -80oC study as previously described (Xiang et al., 2013). Five of the tissues were used in this study: Brain, Liver, Lung, Muscle and Placenta. Three male and three female fetus from each of the 4 genetic types (Bt x Bt; Bi x Bt; Bt x Bi; Bi x Bi; paternal genome listed first) were used in this study for a total of 24 samples per tissue.
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| Contributor(s) |
Liu R, Hiendleder S |
| Citation(s) |
34082698 |
| Submission date |
Apr 19, 2020 |
| Last update date |
Jun 09, 2021 |
| Contact name |
Ruijie Liu |
| E-mail(s) |
cynthia.liu@adelaide.edu.au
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| Organization name |
the university of Adelaide
|
| Street address |
Mudla Wirra Rd
|
| City |
Roseworthy |
| State/province |
South Australia |
| ZIP/Postal code |
5371 |
| Country |
Australia |
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| Platforms (1) |
| GPL23055 |
Illumina NextSeq 500 (Bos taurus) |
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| Samples (116)
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| Relations |
| BioProject |
PRJNA626458 |
| SRA |
SRP257404 |
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