|
| Status |
Public on Jul 23, 2020 |
| Title |
goat_high_lung3 |
| Sample type |
SRA |
| |
|
| Source name |
lung tissue from high-altitude goat
|
| Organism |
Capra hircus |
| Characteristics |
population: Tibetan Goat
tissue: lung
age: > 3 year
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Three adult females (~3 years old) from each of the low-altitude goat and Tibetan goat populations residing at distinct altitudes in southwest China (600 m and 3000 m) were used in this study. Animals were fed with free access to food and water, and killed humanely to ameliorate suffering. All of the animals procedures complied the guidelines for the care and use of experimental animals established by the Ministry of Agriculture of China. Six typical hypoxia-sensitive tissues (heart, kidney, liver, lung, longissimus muscle and spleen) were rapidly excised from the carcass, immediately frozen in liquid nitrogen, and then stored at −80 °C until RNA isolation.
Small RNA libraries were constructed using the Illumina TruSeq Small RNA Sample Prep kit. Libraries were assessed using the Agilent 2200 TapeStation and sequenced on the Illumina HiSeq 2500 platforms.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Incipient bioinformatics analysis (base calling) was performed with CASAVA 1.8 (Illumina) to generate raw reads (in FASTQ form).
Raw reads was subjected to a series of stringent filters (such as removing low quality-reads, repeated sequences and adaptor sequences). Filtered sequences were then mapped to goat reference genome (assembly ARS1) with stringent criteria (0 mismatch in the whole length) using Bowtie. Next, mappable reads were submitted to miRDeep version 2.0.0.7 to detect miRNAs with default parameters, while mature miRNA sequences of goat and all other annotated mammalian species in miRbase release 21 were selected as reference. miRNAs with readcount no less than 3 in at least one sample were remained for further analysis.
Genome_build: goat representative genome (ARS1)
Supplementary_files_format_and_content: expression of identified miRNAs in each library
|
| |
|
| Submission date |
Jan 25, 2019 |
| Last update date |
Jul 23, 2020 |
| Contact name |
Siyuan Feng |
| E-mail(s) |
siyuanfeng.bioinfo@gmail.com
|
| Phone |
15183520327
|
| Organization name |
Sichuan Agriculcural University
|
| Department |
College of Animal Science and Technology
|
| Street address |
Huiming Road #211, Wenjiang District
|
| City |
Chengdu |
| State/province |
Sichuan |
| ZIP/Postal code |
611130 |
| Country |
China |
| |
|
| Platform ID |
GPL19149 |
| Series (1) |
| GSE125665 |
Comparative microRNA Transcriptome in Domestic Goats Reveals Adaptation to High Altitude |
|
| Relations |
| BioSample |
SAMN10819943 |
| SRA |
SRX5291981 |
