|
| Status |
Public on Dec 04, 2010 |
| Title |
[E-MTAB-308] Zebrafish embryo 1 dpf mRNA 3' end |
| Sample type |
SRA |
| |
|
| Source name |
Zebrafish embryo 1 dpf mRNA 3' end
|
| Organism |
Danio rerio |
| Characteristics |
material type: organism_part
strainorline: Tuebingen
age: 1 day
initialtimepoint: fertilization
developmentalstage: embryo
organismpart: whole_organism
Sex: unknown_sex
|
| 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).
specified_biomaterial_action | 20 µg of total RNA was fragmented using RNA Fragmentation Reagent (Ambion) for 5 minutes at 70 C and ethanol precipitated with glycogen and LiCl. RNA was annealed to the oligo stBPM1polyT22 (biotin-GGCCAGTCCTGGAGTTTTTTTTTTTTTTTTTTTTTTVN) and bound to streptavidin magnetic beads. After washing by pull down on a magnet, the bound RNA was reverse transcribed with SuperScript II (Invitrogen) and a second strand synthesised with DNA polymerase I (Promega) and RNase H (NEB). After further washing, the double strand cDNA was released from the beads with BpmI (NEB). The cDNA was recovered with the QIAgen PCR Purification Kit and made into a standard Illumina library following the manufacturerÕs protocol with a fragment size of 250 to 300 bp.
scanning | Base calling was performed using Illumina pipeline 1.3 (Bustard 1.3.4) with phred quality scores at 64 levels using Illumina pipeline 1.3 (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.
sequencing | Sequencing was performed using the Illumina Genome Analyzer II
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Provider: SANGER
|
| Data processing |
processed data not provided
|
| |
|
| Submission date |
Oct 29, 2010 |
| 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) |
| GSE25023 |
[E-MTAB-308] Zebrafish gene 3 prime end pull down for genome annotation |
|
| Relations |
| SRA |
ERX005932 |
