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| Status |
Public on Feb 26, 2016 |
| Title |
in_vivo_group (conventionally bred - RNA) |
| Sample type |
SRA |
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| Source name |
leg muscle
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| Organism |
Sus scrofa |
| Characteristics |
developmental stage: newborn
tissue: leg muscle
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| Growth protocol |
newborn piglets
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from samples of biceps femoris muscle using TRIzol Reagent (Invitrogen).
The concentration and quality of RNA was confirmed using an Agilent 2100 system and agarose gel electrophoresis (AGE). Equal amounts of RNA from the tissue samples of three abnormal cloned piglets, three normal cloned piglets were mixed into three pools. The two independent RNA pools were then used for library construction and sequencing by the Beijing Genome Institute. Briefly, after evaluation of the quality of total RNA, mRNA was enriched by using oligo(dT) magnetic beads. After adding the fragmentation buffer, mRNA was interrupted to short fragments (≈200 bp). First-strand cDNA was synthesized using a random hexamer primer using the mRNA fragments as templates. Then buffer, dNTPs, RNase H and DNA polymerase I were added to synthesize the second strand. Double-strand cDNA was purified with a QiaQuick PCR Extraction kit and washed with Ethidium Bromide buffer for end repair and addition of single nucleotide A (adenine). Finally, sequencing adaptors were ligated to the fragments. Required fragments were purified by AGE and enriched by PCR amplification.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Original data were transferred into sequence data by base calling.
To obtain clean reads, raw reads were filtered before data analyses. First, the adaptors were removed; second, reads in which unknown bases were > 10% were discarded; third, low-quality reads (the percentage of low-quality bases of quality value ≤ 5 in a read were > 50%) were removed. Clean reads were mapped to reference sequences using SOAPaligner/soap2. Mismatches of no more than 2 bases were allowed in the alignment. The message abundance was calculated using the RPKM method.
Genome_build: Sscrofa9.61
Supplementary_files_format_and_content: The processed data is xls file, which contains the GeneID,Uniq_reads_num,Length,Coverage,RPKM,Symbol,Description,Blast nr
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| Submission date |
Jun 18, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Changchun Li |
| E-mail(s) |
lichangchun@mail.hzau.edu.cn
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| Organization name |
Huazhong Agriculture University
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| Street address |
No.1, Shizishan Street · Hongshan District
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| City |
Wuhan |
| State/province |
Hu Bei |
| ZIP/Postal code |
430070 |
| Country |
China |
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| Platform ID |
GPL11429 |
| Series (2) |
| GSE70002 |
Genome-wide gene expression and DNA methylation reveals Genetic and Epigenetic differences in cloned piglets and conventionally bred normal piglets (RNA-Seq) |
| GSE70005 |
Genome-wide gene expression and DNA methylation reveals Genetic and Epigenetic differences in cloned piglets and conventionally bred normal piglets |
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| Relations |
| BioSample |
SAMN03782154 |
| SRA |
SRX1065256 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1715563_in_vivo_group.Gene.rpkm.xls.gz |
776.8 Kb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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