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| Status |
Public on Sep 06, 2017 |
| Title |
3000m_2_muscle |
| Sample type |
SRA |
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| Source name |
muscle
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| Organism |
Capra hircus |
| Characteristics |
location/altitude: A'ba Tibetan autonomous area, Sichuan province, China, 3,000m altitude
tissue: muscle
age: ~3 years old
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| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was extracted using the TrIzol reagent (Life Technologies, Beijing, China) according to the manufacturer’s protocols. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
The dUTP based strand-specific RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
A'ba Tibetan autonomous area, Sichuan province, China, 3,000m altitude
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| Data processing |
Illumina Casava1.82 software was used for basecalling.
High-quality reads were obtained by discarding reads containing over 10% Ns, or overlapping at least 10 bp with adaptor sequences at mismatch rate equal to or less than 10%, or including over 50% bases with base quality score less than five, and then mapped to goat genome using Tophat 2.0.11.
Cufflinks version 2.2.1 were applied to quantify gene expression and obtain FPKM expression values (denoted as the fragments per Kb of transcript per Mb mapped reads). The list of Gene IDs can be obtained from the website http://www.goatgenome.org/projects.html.
Genome_build: goat genome "chinese assembly v2". http://www.goatgenome.org/projects.html
Supplementary_files_format_and_content: tab-delimited text file includes normalized abundance measurements of genes in FPKM values
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| Submission date |
Feb 24, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Mingzhou Li |
| E-mail(s) |
[email protected]
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| Organization name |
Sichuan Agricultural University
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| Street address |
No.211 Huimin Road, Wenjiang District
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| City |
Chengdu |
| State/province |
Sichuan |
| ZIP/Postal code |
611130 |
| Country |
China |
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| Platform ID |
GPL15473 |
| Series (1) |
| GSE66242 |
Transcriptomic analysis provides insights into the high-altitude adaptation in domestic goats |
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| Relations |
| BioSample |
SAMN03381116 |
| SRA |
SRX893900 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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