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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 12, 2017 |
| Title |
YE49_1 |
| Sample type |
SRA |
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| Source name |
Large White, ovary, 49 days post coitus, rep1
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| Organism |
Sus scrofa |
| Characteristics |
breed: Large White
tissue: ovary
time: 49 days post coitus
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the TRIzol Reagent (Invitrogen, Carlsbad, CA, USA). Genomic DNA was removed by DNase I (Qiagen, Beijing, China). The quantity and quality of the RNA were assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, California, USA). Ribosomal RNA was depleted using Ribo-Zero Magnetic kit (Epicentre, Madison, WI ).
Strand-specific RNA libraries for the paired-end sequencing were prepared using SMART protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Adaptors in the total RNA-seq reads were firstly trimmed by custom scripts.
Processed reads from each sample were aligned to the reference genome of Sus scrofa (version 10.2, downloaded from ENSEMBL) by using TopHat v2.1.0.
Assignment of reads to genes was performed using htseq-count
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: Sus scrofa 10.2
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.
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| Submission date |
Sep 29, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Zhonglin Tang |
| E-mail(s) |
zhonglinqy_99@sina.com
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| Phone |
+86-10-62813822
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| Organization name |
Chinese Academy of Agricultural Sciences
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| Department |
Institute of Animal Science
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| Lab |
Department of Gene and Cell Engineering
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| Street address |
No. 2 Yuanmingyuan West Road, Beijing, 100193, P.R.China,
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| City |
Beijing |
| ZIP/Postal code |
100193 |
| Country |
China |
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| Platform ID |
GPL19176 |
| Series (1) |
| GSE73593 |
Total RNA sequencing of ovary tissues at 49 days post coitus in Large White and Meishan pigs. |
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| Relations |
| BioSample |
SAMN04123125 |
| SRA |
SRX1295813 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1898696_Y1.RPKM.txt.gz |
281.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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