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| Status |
Public on Sep 29, 2023 |
| Title |
Tibpika-3 |
| Sample type |
SRA |
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| Source name |
Tibetan pika fibroblast
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| Organism |
Ochotona curzoniae |
| Characteristics |
tissue: epidermis
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| Growth protocol |
Cells were cultured under 5% CO2, 37 ℃ with DMEM (10% FBS, 1% PS)
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| Extracted molecule |
total RNA |
| Extraction protocol |
After growing to 90% confluency, cells were lysed with TRIZOL directly and total RNA was extracted with chloroform and isopropanol.
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 |
HiSeq X Ten |
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| Data processing |
Basecalls performed using CASAVA version 1.9
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 (for mouse), Rnor6 (for rat), OryCun2 (for rabbit),OchPri3 (for pika) whole genome using STAR v2.6.1a with default parameters
Fragments Per Kilobase of exon per Megabase of library size (RPKM) were calculated using featureCounts function from Rsubread (v2.0.1) and rpkm function of edgeR (v3.28.1). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCm38, Rnor6, OryCun2, OchPri3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
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| Submission date |
Oct 26, 2020 |
| Last update date |
Sep 29, 2023 |
| Contact name |
wang jiawen |
| E-mail(s) |
wangjiawen2013@gmail.com
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| Organization name |
National institute of biological sciences
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| Street address |
7 Science Park Road ZGC Life Science Park
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| City |
Beijing |
| ZIP/Postal code |
102206 |
| Country |
China |
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| Platform ID |
GPL29306 |
| Series (1) |
| GSE158760 |
ChIP-seq data from pika Epas1 knock in MAF and RNA-seq data from mouse, rat, rabbit and Tibetan pika fibroblasts |
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| Relations |
| BioSample |
SAMN16560291 |
| SRA |
SRX9366707 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4861857_pika-3.txt.gz |
140.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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