run_metadata: 37223

This data as json

rowid	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.r4_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	tech_variant	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
37223	SRR1035982	SRX381836	SRS506053	SRP033261	PRJNA229539	Whole transcriptomic sequencing of zebrafish rx3 mutants during optic vesicle morphogenesis	GSE52652	Transcriptome Analysis	To identify genes regulated by Rx3 during optic vesicle morphogenesis adult zebrafish carriers of a null rx3 mutation were mated. Before 13 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		pubmed:25266257		Wild type siblings rep2	GSM1273588		source name:Whole embryo\|strain:AB\|tissue:Whole embryo\|age:13 hpf\|genotype:Wild type siblings	Wild type siblings rep2	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.	Whole embryo		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.	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.	strain:AB\|tissue:Whole embryo\|age:13 hpf\|genotype:Wild type siblings	GSM1273588	GSM1273588: Wild type siblings rep2; Danio rerio; RNA Seq	GSM1273588		1	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.	GEO Accession:GSM1273588	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer II		SRP033261			Sib2.fastq	fastq	878040360.0	21951009.0	GSM1273588 r1	0:40	A:227146795;C:213249395;G:206995607;T:230550546;N:98017	40				227146795	213249395	206995607	230550546	98017	SRX381836	SRS506053	SRA112080	GEO	Kennedy Lab, UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin	1	0.93985		0.06787		0.72535		0.46201		40		B		usable mapping rate	illumina	early_illumina	full_length	poly_a	unknown	bulk	bulk	bulk		Ireland	2013-11-22	Segmentation	Embryo	Whole Organism	All anatomical structures