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| Status |
Public on Nov 29, 2013 |
| Title |
DSQ-RNA-muscle |
| Sample type |
SRA |
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| Source name |
DSQ_muscle_RNA-seq
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| Organism |
Pseudopodoces humilis |
| Characteristics |
tissue: muscle
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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 libraries.
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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| Data processing |
Illumina Casava1.82 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Ground tit 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: Ground tit genome assembly (PRJNA179234 available on Mar 1, 2014)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.
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| Submission date |
Mar 01, 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 |
GPL16735 |
| Series (1) |
| GSE44779 |
Pseudopodoces humilis Transcriptome data used for gene annotation |
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| Relations |
| SRA |
SRX246872 |
| BioSample |
SAMN01933047 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1091210_muscle-2.transcripts.gff.gz |
2.0 Mb |
(ftp)(http) |
GFF |
| GSM1091210_muscle-3.transcripts.gff.gz |
1.9 Mb |
(ftp)(http) |
GFF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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