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| Status |
Public on Sep 06, 2017 |
| Title |
goat_kidney_3 |
| Sample type |
SRA |
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| Source name |
kidney
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| Organism |
Capra hircus |
| Characteristics |
strain: indigenous
location: Ya'an, Sichuan province, China
tissue: kidney
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; Strand-specific mRNA-Seq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
TSY_shen3
processed data file: goat_PCA_new.txt
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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.
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).
Genome_build: cattle: bosTau6 or UMD3.1, sheep: oviAri3, goat: chinese assembly v2 (http://www.goatgenome.org/projects.html)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample. The goat protein sequences are available in the file goat.v4.gff.filter.pep.txt on the series record.
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| Submission date |
Jan 20, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Mingzhou Li |
| E-mail(s) |
mingzhou.li@163.com
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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 |
GPL19149 |
| Series (1) |
| GSE77020 |
Multi-tissue RNA-seq data across three species |
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| Relations |
| BioSample |
SAMN04430424 |
| SRA |
SRX1538145 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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