{"database": "metadata", "table": "run_metadata", "rows": [[37907, "SRR1104969", "SRX424037", "SRS527958", "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", null, "108hpf clbn", "GSM1303831", null, "source name:108hpf clbn larvae|genotype/variation:clbns841|development stage:108 hpf|tissue:whole larvae", "108hpf clbn", "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 clbn 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\u2122 Whole Transcriptome Analysis Kit with protocol Part Number 4409491 Rev F  08/2009. 8\u03bcl of polyA RNA were was fragmented by incubating with RNase III for 10min at 37\u00b0C and immediately purified on Qiagen RNeasy columns. Samples were eluted in 50\u03bcl of nuclease free water and the columns incubated for 10min before the final centrifugation. Samples were concentrated to a volume of 5\u03bcl by centrifuging under vacuum at 40\u00b0C. 1\u03bcl 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\u2019 end of the sense strand. post o/n ligation  samples were reverse transcribed for 30min at 42\u00b0C 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\u00b0C incubator on a 12h light/dark cycle.", "genotype/variation:clbns841|developmental stage:108 hpf|tissue:whole larvae", "GSM1303831", "GSM1303831: 108hpf clbn; Danio rerio; RNA Seq", "GSM1303831", null, "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\u2122 Whole Transcriptome Analysis Kit with protocol Part Number 4409491 Rev F  08/2009. 8\u03bcl of polyA RNA were was fragmented by incubating with RNase III for 10min at 37\u00b0C and immediately purified on Qiagen RNeasy columns. Samples were eluted in 50\u03bcl of nuclease free water and the columns incubated for 10min before the final centrifugation. Samples were concentrated to a volume of 5\u03bcl by centrifuging under vacuum at 40\u00b0C. 1\u03bcl 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\u2019 end of the sense strand. post o/n ligation  samples were reverse transcribed for 30min at 42\u00b0C 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:GSM1303831", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP035264", null, null, "108hpf_clbn_F3_QV.qual.bz2 108hpf_clbn_F3.csfasta.bz2", "SOLiD_native SOLiD_native", 2698882700.0, 53977654.0, "GSM1303831 r1", "0:50", "0:653022205;1:711705790;2:753066133;3:571973990;.:9114582", 50, null, null, null, null, null, null, null, null, "SRX424037", "SRS527958", "SRA123959", "GEO", "Heath Laboratory, Development and Cancer, Walter and Eliza Hall Institute of Medical Research", 1, 0.56134, null, 0.05842, null, 0.84303, null, 0.49093, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2014-01-09", "Larval", "Larval", "Whole Organism", "All anatomical structures"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["37907"], "units": {}, "query_ms": 10.857564004254527}