|
| Status |
Public on Dec 14, 2013 |
| Title |
RNA-seq 256-cell |
| Sample type |
SRA |
| |
|
| Source name |
embryos
|
| Organism |
Danio rerio |
| Characteristics |
developmental stage: 2.5 hpf (256-cell stage)
|
| Growth protocol |
Zebrafish were maintained and raised under standard conditions. Wild-type embryos were collected at the 1-cell stage, synchronized and allowed to develop to the desired stage at 28°C.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated using the standard Trizol (Invitrogen) protocol. Two rounds of PolyA+-RNA purification were performed for each sample, using the PolyA(Purist)TM-MAG kit (Ambion). The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bioanalyzer. Strand-specific libraries for 76 bp paired-end sequencing were prepared according to a modified UTP-method (Parkhomchuk et al. 2009), as detailed in (Levin et al. 2010).
Libraries were prepared using the Illumina sequencing library preparation protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 1
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to zv9 whole genome using tophat v1.1.4 with parameters --mate-inner-dist 200 --mate-std-dev=18 --solexa-quals --library-type fr-unstranded --no-novel-juncs.
RPKM were calculated using Cufflinks v1.1.0 with parameters --frag-bias-correct --multi-read-correct.
Genome_build: zv9
Supplementary_files_format_and_content: Tab-delimited text file include abundance measurements (RPKM values) and corresponding Ensembl gene IDs.
|
| |
|
| Submission date |
Dec 14, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Yong Zhang |
| Organization name |
Tongji University
|
| Street address |
1239 Siping Road
|
| City |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
| |
|
| Platform ID |
GPL14875 |
| Series (1) |
| GSE44269 |
Canonical Nucleosome Organization at Promoters Forms During Genome Activation |
|
| Relations |
| BioSample |
SAMN02444269 |
| SRA |
SRX391998 |
