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| Status |
Public on Sep 30, 2014 |
| Title |
Wild-type siblings rep1 |
| Sample type |
SRA |
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| Source name |
Whole embryo
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| Organism |
Danio rerio |
| Characteristics |
strain: AB
tissue: Whole embryo
age: 13 hpf
genotype: Wild-type siblings
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| Growth protocol |
Zebrafish were handled according to standard protocols and animals studies were approved by the UCD Animal Research Ethics Committee (AREC-P-08-54). Heterozygous carriers of a recessive rx3 mutation (chkw29 allele) were mated. These fish originate from mutagenesis screens performed in AB zebrafish. Offspring were grown to the 13 hpf stage in embryo medium containing methylene blue at 28.5°C in 10 hour dark: 14 hour light cycle conditions. The eyeless mutant (rx3-/-) and eyed sibling (wild-type rx3+/+ and heterozygous rx3+/- carriers) samples were distinguished based on their morphology using a dissecting light microscope at the 8-somite stage.
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| Extracted molecule |
total RNA |
| Extraction 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
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| Data processing |
Due to low sequencing quality at 3’ ends, RNA-seq reads were trimmed at 40 bp. Reads were mapped to the zebrafish genome version 9 using TopHat. Novel transcripts were assembled by Cufflinks using mapped reads. Novel transcripts less than 300 bp were discarded. RNA-seq reads were counted using HTSeq.
Genome_build: Zv9
Supplementary_files_format_and_content: counts.txt: Tab-delimited text files include gene symbol, chromosome location and No. of mapped reads and RPKM for each sample.
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| Submission date |
Nov 22, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Breandan Kennedy |
| E-mail(s) |
brendan.kennedy@ucd.ie
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| Organization name |
UCD Conway Institute, University College Dublin
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| Department |
UCD School of Biomolecular and Biomedical Science
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| Lab |
Kennedy Lab
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| Street address |
Belfield
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| City |
Dublin |
| ZIP/Postal code |
Dublin 4 |
| Country |
Ireland |
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| Platform ID |
GPL9319 |
| Series (1) |
| GSE52652 |
Whole transcriptomic sequencing of zebrafish rx3 mutants during optic vesicle morphogenesis |
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| Relations |
| BioSample |
SAMN02419472 |
| SRA |
SRX381835 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1273587_Sib1_counts.txt.gz |
614.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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