|
| Status |
Public on Jul 14, 2011 |
| Title |
[E-MTAB-434] RNA from Zebrafish embryo 3 dpf |
| Sample type |
SRA |
| |
|
| Source name |
Zebrafish embryo 3 dpf
|
| Organism |
Danio rerio |
| Characteristics |
material type: whole_organism
Sex: mixed
age: 3 days
developmentalstage: embryo
stainorline: Tuebingen
organismpart: whole organism
|
| Growth protocol |
grow | Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at -70 C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
nucleic_acid_extraction | Total RNA was extracted using Trizol Reagent (Invitrogen) following the manufacturer's instructions. Pellets were resuspended RNase-free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND-1000 Spectrophotometer (Axon Instruments). Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp.
scanning | Base calling was performed using Illumina pipeline 1.8.67.0 (Bustard 1.8.1a1) with phred quality scores at 64 levels using Illumina pipeline 1.8.67.0 (GERALD). There were 152 cycles of sequencing with 2 reads per cluster, a forward read starting at base 1 and a reverse read starting at base 77.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Performer: SC
|
| Data processing |
processed data not provided
|
| |
|
| Submission date |
Jul 12, 2011 |
| Last update date |
May 15, 2019 |
| Organization |
European Bioinformatics Institute |
| E-mail(s) |
miamexpress@ebi.ac.uk
|
| Lab |
ArrayExpress
|
| Street address |
Wellcome Trust Genome Campus
|
| City |
Hinxton |
| State/province |
Cambridgeshire |
| ZIP/Postal code |
CB10 1SD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL9319 |
| Series (1) |
| GSE30603 |
[E-MTAB-434] Transcription profiling by high throughput sequencing of zebra fish tissues and developmental stages |
|
| Relations |
| SRA |
ERX008921 |
