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SRX381835: GSM1273587: Wild-type siblings rep1; Danio rerio; RNA-Seq
1 ILLUMINA (Illumina Genome Analyzer II) run: 22.9M spots, 915.3M bases, 481.1Mb downloads

Submitted by: Gene Expression Omnibus (GEO)
Study: Whole transcriptomic sequencing of zebrafish rx3 mutants during optic vesicle morphogenesis
show Abstracthide Abstract
To identify genes regulated by Rx3 during optic vesicle morphogenesis, adult zebrafish carriers of a null rx3 mutation were mated. Before 13 hours post fertilization (hpf), the earliest time point at which optic vesicle evagination phenotypes could be reliably detected, offspring were phenotypically separated into pools comprising of mutants with an absence of optic vesicles or siblings exhibiting a wild-type phenotype. Three replicates of pooled RNA samples from 13 hpf eyeless mutants (rx3-/-) or phenotypically wild-type siblings (rx3+/+ or rx3+/-), and one replicate of 13 hpf wild-type zebrafish larva were collected for whole transcriptome sequencing. Overall design: Whole transcriptome sequencing (RNA-seq) was performed on zebrafish rx3-/- mutants, wild-type siblings and wild-type AB strains at 13 hpf
Sample: Wild-type siblings rep1
SAMN02419472 • SRS506052 • All experiments • All runs
Organism: Danio rerio
Instrument: Illumina Genome Analyzer II
Strategy: RNA-Seq
Selection: cDNA
Layout: SINGLE
Construction protocol: Three biological replicates were collected for each sample and one replicate of wild-type (AB strain) embryos at the same developmental stage was collected. Each replicate contained pools of 10 whole embryos. Samples were collected in RNAlater (Qiagen, Hilden, Germany) and stored at 4°C until processing. The RNeasy mini RNA extraction kit was used to isolate RNA, on-column DNaseI digestion was performed and RNA was collected in RNase-free water, as per manufacturer’s instructions (Qiagen, Hilden, Germany). A Nanodrop spectrophotometer (Beckman, USA) was used to determine the concentration of RNA and a Bioanalyser (Agilent, Santa Clara, USA) was used to confirm the RNA Integrity Number (RIN) of the samples as 8 or higher. Using 1 μg of total RNA, cDNA libraries were prepared using the mRNA-seq 8-Sample Prep Kit as per manufacturer’s instructions (Illumina, RS-100-0801). Briefly, poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, mRNA was fragmented and cDNA generated with ligated adaptors. These products were purified and PCR enriched to create the final cDNA library.
Experiment attributes:
GEO Accession: GSM1273587
External link:
Runs: 1 run, 22.9M spots, 915.3M bases, 481.1Mb
Run# of Spots# of BasesSizePublished


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