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| Status |
Public on Dec 24, 2014 |
| Title |
sham |
| Sample type |
SRA |
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| Source name |
heart
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| Organism |
Danio rerio |
| Characteristics |
tissue: heart
developmental stage: adult
strain: TL
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| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted using QIAGEN RNeasy Microarray Tissue Mini Kit (Cat No. 73304)
Poly (A)-positive RNA was purified with the Dynabeads mRNA purification kit (Invitrogen) from 5μg of total RNA with high quality (RNA integrity number >7.5), following the manufacturer's instructions. A strand-specific RNA-Seq library preparation on the basis of the incorporation of deoxy-UTP was performed; Exome fragments were captured and enriched by SureSelect Human All Exon 50 Mb kits (Agilent Technologies) following the manufacture’s protocol.
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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 |
Sequenced reads were filtered by in-house pipeline to remove low-quality and unclear base containing reads, then mapped to danRer7 by tophat v1.4.0 with parameters --mate-inner-dist 100 --solexa1.3-quals --coverage-search --microexon-search --library-type fr-firststrand
Differential expression were performed by Cuffdiff v2.0.2 with paremeters --compatible-hits-norm --multi-read-correct --library-type fr-firststrand
Genome_build: danRer7
Supplementary_files_format_and_content: Table format as Cuffdiff results.
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| Submission date |
Aug 26, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Shouyu Yan |
| E-mail(s) |
Yan.Shouyu@gmail.com
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| Organization name |
Peking University
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| Department |
Institution of Molecular Medicine
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| Street address |
5#, Yiheyuan Road
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| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platform ID |
GPL14875 |
| Series (1) |
| GSE50203 |
Transcriptome analysis of heart regeneration in adult zebrafish |
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| Relations |
| BioSample |
SAMN02334702 |
| SRA |
SRX339606 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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