run_metadata: 37908

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
37908	SRR1104968	SRX424036	SRS527957	SRP035264	PRJNA236557	Genome wide analysis of gene expression and intron retention during development in a U12 type splicing deficient zebrafish mutant [RNA seq]	GSE53758	Transcriptome Analysis	To determine the global impact of the clbn mutation on gene expression and efficiency of U2 and U12 type splicing we analyzed the transcriptome of 108hpf wt and clbn mutant larvae by microarrays and RNA sequencing. RNAseq data was used to characterize intron retention of U2 type and U12 type intron on a genome wide scale to confirm that rnpc3 deficiency specifically impairs U12 type splicing. RNAseq and microarray data were combined to yield high confidence lists of differentially expressed genes which show that impaired U12 type splicing has a wide ranging effect on the developing transcriptome. Overall design: RNAseq libraries prepared from 108 hpf zebrafish larvae approx. 60 embryos each genotyped homozygous wildtype and homozygous clbns841 mutants respectively	parent bioproject:PRJNA236230	pubmed:24516132		108hpf wt	GSM1303830		source name:108hpf wt larvae\|genotype/variation:wildtype\|development stage:108 hpf\|tissue:whole larvae	108hpf wt	50bp single end reads were mapped using the X MATE recursive mapping pipeline 42 allowing for 5 color space mismatches per 50bp read CS 50 5 The uniquely mappable regions uniqueome of the ZV9 assembly were calculated using the same mapping parameters CS 50 5 For intron retention analysis RPKM were calculated for annotated Refseq introns + manually annotated U12 type introns using Galaxy For gene expression analysis RPKM were calculated for annotated Refseq coding regions using Galaxy Genome build: Zebrafish Zv9	108hpf wt larvae	Starting at 24 hpf embryos were transferred into egg water containing 0.003% 1 Phenyl 2 thiourea PTU to prevent pigmentation	Genomic DNA and total RNA were extracted concurrently form single embryos by acid guanidinium thiocyanate phenol chloroform extraction. Genomic DNA extraction and genotyping of individual embryos was completed first and aqueous phases of all homozygous wildtype and mutant larvae respectively were pooled prior to RNA precipiation with isopropanol. For RNA sequencing RNA was extracted from approx 60 pooled genotyped larvae and subsequently enriched for polyA RNA by two successive rounds of polyA selection with the MicroPolyAPurist Kit Ambion. Libraries for deep sequencing were generated using the SOLiD™ Whole Transcriptome Analysis Kit with protocol Part Number 4409491 Rev F 08/2009. 8μl of polyA RNA were was fragmented by incubating with RNase III for 10min at 37°C and immediately purified on Qiagen RNeasy columns. Samples were eluted in 50μl of nuclease free water and the columns incubated for 10min before the final centrifugation. Samples were concentrated to a volume of 5μl by centrifuging under vacuum at 40°C. 1μl of each sample was analysed on the Agilent Bioanalyzer Agilent using an RNA Nano 6000 chip Agilent to assess quantity and size distribution of the fragmented RNA. The fragmented RNA was hybridised and ligated to Adaptor Mix A to generate templates for SOLiD System sequencing from the 5’ end of the sense strand. post o/n ligation samples were reverse transcribed for 30min at 42°C and the obtained cDNA purified using Qiagen inElute PCR Purification Kit. 100 200bp fragments were size selected by excision from a 6% polyacrylamide 8M urea TBE gels. cDNA in gel slices was subjected to 18 cycles of amplification and purified using PureLink PCR Micro columns Invitrogen. The majority of cDNAs in the library was between 150 and 250bp in size and less than 2 8% of cDNAs fell in the 25 150bp size range as per protocol requirements. The finished cDNA libraries were used for attachment to beads by emulsion PCR.	Embryos for all experiments were produced by natural spawning transferred into petri dishes with pre warmed egg water 60mg of sea salt/1L ddH20 and placed in a 28.5°C incubator on a 12h light/dark cycle.	genotype/variation:wildtype\|developmental stage:108 hpf\|tissue:whole larvae	GSM1303830	GSM1303830: 108hpf wt; Danio rerio; RNA Seq	GSM1303830		1	Genomic DNA and total RNA were extracted concurrently form single embryos by acid guanidinium thiocyanate phenol chloroform extraction. Genomic DNA extraction and genotyping of individual embryos was completed first and aqueous phases of all homozygous wildtype and mutant larvae respectively were pooled prior to RNA precipiation with isopropanol. For RNA sequencing RNA was extracted from approx 60 pooled genotyped larvae and subsequently enriched for polyA RNA by two successive rounds of polyA selection with the MicroPolyAPurist Kit Ambion. Libraries for deep sequencing were generated using the SOLiD™ Whole Transcriptome Analysis Kit with protocol Part Number 4409491 Rev F 08/2009. 8μl of polyA RNA were was fragmented by incubating with RNase III for 10min at 37°C and immediately purified on Qiagen RNeasy columns. Samples were eluted in 50μl of nuclease free water and the columns incubated for 10min before the final centrifugation. Samples were concentrated to a volume of 5μl by centrifuging under vacuum at 40°C. 1μl of each sample was analysed on the Agilent Bioanalyzer Agilent using an RNA Nano 6000 chip Agilent to assess quantity and size distribution of the fragmented RNA. The fragmented RNA was hybridised and ligated to Adaptor Mix A to generate templates for SOLiD System sequencing from the 5’ end of the sense strand. post o/n ligation samples were reverse transcribed for 30min at 42°C and the obtained cDNA purified using Qiagen inElute PCR Purification Kit. 100 200bp fragments were size selected by excision from a 6% polyacrylamide 8M urea TBE gels. cDNA in gel slices was subjected to 18 cycles of amplification and purified using PureLink PCR Micro columns Invitrogen. The majority of cDNAs in the library was between 150 and 250bp in size and less than 2 8% of cDNAs fell in the 25 150bp size range as per protocol requirements. The finished cDNA libraries were used for attachment to beads by emulsion PCR.	GEO Accession:GSM1303830	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB SOLiD System 3.0		SRP035264			108hpf_wt_F3_QV.qual.bz2 108hpf_wt_F3.csfasta.bz2	SOLiD_native SOLiD_native	2835473700.0	56709474.0	GSM1303830 r1	0:50	0:697915785;1:748317376;2:781024795;3:605838541;.:2377203	50									SRX424036	SRS527957	SRA123959	GEO	Heath Laboratory, Development and Cancer, Walter and Eliza Hall Institute of Medical Research	1	0.57033		0.05759		0.8384		0.49692		50		B		usable mapping rate	legacy	early	full_length	poly_a	unknown	bulk	unknown	unknown		Australia	2014-01-09	Larval	Larval	Whole Organism	All anatomical structures