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| Status |
Public on Feb 09, 2017 |
| Title |
tissue-mixure |
| Sample type |
SRA |
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| Source name |
multiple tissues
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| Organism |
Sus scrofa |
| Characteristics |
breed: multiple breeds
age: multiple time points
tissue: multiple tissues
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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 ). The mixed libraries were constructed by mixing equal quantities of each RNA sample. Strand-specific libraries for the paired-end sequencing were prepared using SMART or dUTP protocol.
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 Genome Analyzer II |
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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 (version 1.3.2). Parameters were set for strand-specific mapping (--library-type ‘fr-second strand’ for SMART protocol and 'fr-first strand' for dUTP protocol).
Mapped reads from each sample were assembled into transcripts independently by using Cufflinks,also with the assistance of known annotations.Putative transcripts were retrieved with the parameter '--min-frags-per-transfrag 3'.
assembled transcripts from each sample were merged into a consensus transcriptome by using Cuffmerge
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 |
Oct 06, 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 |
GPL10945 |
| Series (1) |
| GSE73763 |
Total RNA sequencing in multiple Sus Scrofa tissues reveals novel long non-coding RNAs functioning in skeletal muscle development |
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| Relations |
| BioSample |
SAMN04147107 |
| SRA |
SRX1307224 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1902356_tissue_mixture.RPKM.txt.gz |
319.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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