|
| Status |
Public on Dec 06, 2013 |
| Title |
wt zebrafish heart |
| Sample type |
SRA |
| |
|
| Source name |
heart
|
| Organism |
Danio rerio |
| Characteristics |
strain background: AB
development stage: 48 hpf
genotype/variation: wt (wild type)
tissue: heart
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs from wild-type and kctd10 mutant fish hearts were isolated with RNeasy Mini Kit (Qiagen), purified with RNeasy columns (QIAGEN).
Next generation sequencing libraries were prepared with the Illumina TruSeq preparation kit (Illumina) according to manufacturer's protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
sequenced by the Illumina Hiseq 2000 platform
Around 200 million 50-bp single-end reads were obtained per sample.
Reads were aligned to zebrafish genome Zv9 using tophat, with up to 2 mismatches allowed.
Differential expression analysis was performed using DESeq.
Genome_build: zebrafish genome Zv9
Supplementary_files_format_and_content: excel file of relative gene expression level between the wt and the kctd10 mutant.
Supplementary_files_format_and_content: tab delimited txt files of gene raw counts and DESeq processed relative gene expression level between the wt and the kctd10 mutant.
|
| |
|
| Submission date |
Dec 05, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiangjun Tong |
| E-mail(s) |
xiangjuntong@pku.edu.cn
|
| Phone |
86-10-62750780
|
| Organization name |
Peking University
|
| Department |
College of Life Sciences
|
| Street address |
Yiheyuan Road No. 5
|
| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
| |
|
| Platform ID |
GPL14875 |
| Series (1) |
| GSE53022 |
Expression profiling in the heart of wild-type and kctd10 mutant zebrafish larvae |
|
| Relations |
| BioSample |
SAMN02437284 |
| SRA |
SRX387597 |
