run_metadata: 77328
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 77328 | SRR065196 | SRX026482 | SRS114569 | SRP003472 | PRJXX3472 | RNA Seq analysis in mutant zebrafish reveals role of U1C protein in alternative splicing regulation | ZF_U1C | Transcriptome Analysis | Precise five prime splice site recognition is essential for both constitutive and regulated pre mRNA splicing. The U1 snRNP specific protein U1C is involved in this first step of spliceosome assembly and important for stabilizing early splicing complexes. We used an embryonically lethal U1C knockout mutant zebrafish hi1371 to investigate the potential genomewide role of U1C for splicing regulation. Surprisingly genomewide RNA Seq analysis of mutant versus wildtype embryos revealed a large set of specific target genes that changed their alternative splicing patterns in the absence of U1C. In sum our findings provide evidence for a new role of a general snRNP protein U1C as a mediator of alternative splicing regulation. | pubmed:21468032 | Total RNA from 3 dpf wildtype zebrafish embryos was prepared by TRIzol reagent Invitrogen and RNeasy kit QIAGEN. Equal amounts of total RNA were subjected to reverse transcription using the qScript cDNA synthesis kit Quanta Biosciences. Control reactions were done in the absence of reverse transcriptase. Total RNA was processed by Illumina standard protocols to prepare the RNA Seq library. | Total RNA from 3 dpf wildtype zebrafish embryos | WT | 3 dpf wildtype embryos | WT | wt | 1 | RNA-Seq | TRANSCRIPTOMIC | RT-PCR | SINGLE | ILLUMINA | Illumina Genome Analyzer II | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | SRP003472 | WT_1.txt.tar WT_2.txt.tar.gz WT_3.txt.tar.gz WT_4.txt.tar.gz | fastq fastq fastq fastq | 2697785376.0 | 35497176.0 | WT | 0:76 | A:676186765;C:669131645;G:670872323;T:676745206;N:4849437 | 76 | 676186765 | 669131645 | 670872323 | 676745206 | 4849437 | SRX026482 | SRS114569 | Justus-Liebig University Giessen | 1 | 0.9435 | 0.087 | 0.71429 | 0.46075 | 76 | B | usable mapping rate | illumina | early_illumina | unknown | other | unknown | bulk | unknown | unknown | Germany | 2011-03-31 | Larval | Larval | Embryo Imprecise | All anatomical structures |