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| Status |
Public on Oct 19, 2014 |
| Title |
GSM-RNA |
| Sample type |
SRA |
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| Source name |
mixed tissues
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| Organism |
Rhinopithecus roxellana |
| Characteristics |
tissue: mixed
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| Extracted molecule |
total RNA |
| Extraction protocol |
Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing library.
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 HiSeq 2000 |
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| Description |
Golden snub-nosed monkey.
Tissues of heart, liver, kidney, spleen, lung, pancreas, muscle and tongue from one individual.
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| Data processing |
Illumina Casava 1.82 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Golden snub-nosed monkey whole genome using Tophat.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads 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: Golden snub-nosed monkey genome assembled by WGS reads using SOAPdenovo software (BioProject: PRJNA230020).
Supplementary_files_format_and_content: Tab-delimited text file includes RPKM values.
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| Submission date |
Dec 23, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Shilin Tian |
| E-mail(s) |
tianshilin@novogene.cn
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| Phone |
13716486614
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| Organization name |
Novogene Bioinformatics Technology CO.ltd
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| Department |
genome research
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| Street address |
Xueqing Road
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| City |
Bei Jing |
| ZIP/Postal code |
100083 |
| Country |
China |
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| Platform ID |
GPL18105 |
| Series (1) |
| GSE53597 |
Golden snub-nosed monkey transcriptome data used for gene annotation |
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| Relations |
| BioSample |
SAMN02485430 |
| SRA |
SRX398287 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1296597_GSM.rpkm.txt.gz |
459.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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