|
| Status |
Public on Jul 14, 2011 |
| Title |
[E-MTAB-460] Zebrafish adult head kidney, 5625_3 |
| Sample type |
SRA |
| |
|
| Source name |
Zebrafish adult head kidney
|
| Organism |
Danio rerio |
| Characteristics |
material type: organism_part
organismpart: head kidney
strainorline: Singapore
Sex: mixed
developmentalstage: adult
|
| Growth protocol |
grow | Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. 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 re-suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND-1000 Spectrophotometer (Axon Instruments).
specified_biomaterial_action | Total RNA was enriched for polyA+ RNA by 2 rounds of polyA pull down with magnetic beads and included a DNase treatment between the 2 rounds. RNA was chemically fragmented, LiCl precipitated, reverse transcribed with random primers, a second strand synthesized and made into a standard Illumina library with a fragment size of 250 to 300 bp.
sequencing | Sequencing was carried out according to the standard Illumina protocol, performed at the Wellcome Trust Sanger Institute.
SRF file were generated using the standard method for the Illumina platform. Base calling was performed using Illumina RTA pipeline 1.8.70.0 (Bustard 1.8.1a2) with phred quality scores at 64 levels using Illumina pipeline 1.8.70.0 (GERALD). There were 160 cycles of sequencing with two 76 base reads per cluster along with an unused 8 base barcode tag. The forward read starts at cycle 1 and the reverse read starts at cycle 85. The sequence in cycles 77 to 84 is only present for technical reasons and should be ignored.
nucleic_acid_extraction | Total RNA was extracted using Trizol Reagent (Invitrogen) following the manufacturer's instructions. Pellets were re-suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND-1000 Spectrophotometer (Axon Instruments).
specified_biomaterial_action | Total RNA was enriched for polyA+ RNA by 2 rounds of polyA pull down with magnetic beads and included a DNase treatment between the 2 rounds. RNA was chemically fragmented, LiCl precipitated, reverse transcribed with random primers, a second strand synthesized and made into a standard Illumina library with a fragment size of 250 to 300 bp.
sequencing | Sequencing was carried out according to the standard Illumina protocol, performed at the Wellcome Trust Sanger Institute.
|
| |
|
| 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) |
[email protected]
|
| 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) |
| GSE30608 |
[E-MTAB-460] Sanger_zebrafish_sequencing |
|
| Relations |
| SRA |
ERX013537 |
