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Sample GSM614642 Query DataSets for GSM614642
Status Public on Dec 04, 2010
Title [E-MTAB-308] Zebrafish adult male body mRNA 3' end
Sample type SRA
 
Source name Zebrafish adult male body mRNA 3' end
Organism Danio rerio
Characteristics material type: organism_part
strainorline: Tuebingen
age: n/a
initialtimepoint: fertilization
developmentalstage: adult
organismpart: whole fish without head or testis
Sex: male
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 ERX005928

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not provided for this record

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