|
| Status |
Public on Nov 13, 2014 |
| Title |
Wildtype Replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
whole head
|
| Organism |
Danio rerio |
| Characteristics |
develolpmental stage: 5 days post fertilization embryo
tissue: whole head
|
| Growth protocol |
Zebrafish embryos from natural matings were maintained at 28C in 6 or 10cm dishes. 5 days post fertilization, the heads of 80-100 embryos per replicate were obtained for RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol (Invitrogen) extraction per manufactor's instructions
Strand-specific, polyA selected RNA-Seq libraries were constructed using a custom dUTP method similar to the standard Illumina protocols, with the addition of 1ul of a 1:10 dilution of ERCC RNA spike-ins prior to polyA selection.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.5
Alignment was performed with Gsnap v2012-07-20 using default parameters and the zv9 genome/transcriptome from Ensembl
Accurate dose response was verified with custom analysis tools and the included ERCC RNA spike-ins
Aligned reads were quantified with Cufflinks v2.1.0 using default parameters and the zv9 transcriptome from Ensembl
Genome_build: zv9
Supplementary_files_format_and_content: Cufflinks v2.1.0 genes.fpkm_tracking
|
| |
|
| Submission date |
Nov 12, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael E. Talkowski |
| E-mail(s) |
talkowski@chgr.mgh.harvard.edu
|
| Organization name |
Massachusetts General Hospital
|
| Department |
Center for Human Genetic Research
|
| Street address |
185 Cambridge Street
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
| |
|
| Platform ID |
GPL14875 |
| Series (1) |
| GSE63191 |
RNA sequencing of the developing zebrafish head |
|
| Relations |
| BioSample |
SAMN03176902 |
| SRA |
SRX757981 |
