run_metadata: 46212
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 |
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| 46212 | SRR6477200 | SRX3567064 | SRS2838996 | SRP129892 | PRJNA430431 | RES complex is associated with intron definition and required for zebrafish early embryogenesis | PRJNA430431 | Other | Pre mRNA splicing is a critical step of gene expression in eukaryotes. Transcriptome wide splicing patterns are complex and primarily regulated by a diverse set of recognition elements and associated RNA binding proteins. The retention and splicing RES complex is formed by three different proteins Bud13p Pml1p and Snu17p and is involved in splicing in yeast. However the importance of the RES complex for vertebrate splicing the intronic features associated with its activity and its role in development are unknown. In this study we have generated loss of function mutants for the three components of the RES complex in zebrafish and showed that they are required during early development. The mutants showed a marked neural phenotype with increased cell death in the brain and a decrease in differentiated neurons. Transcriptomic analysis of bud13 snip1 pml1 and rbmx2 snu17 mutants revealed a global defect in intron splicing with strong mis splicing of a subset of introns. We found these RES dependent introns were short rich in GC and flanked by GC depleted exons all of which are features associated with intron definition. Using these features we developed and validated a predictive model that classifies RES dependent introns. Altogether our study uncovers the essential role of the RES complex during vertebrate development and provides new insights into its function during splicing. | RNAseq Bud13 Bud13 KO 30h | RNAseq Bud13 Bud13 KO 30h AG01144 | strain:TU/AB|age:30.0|dev stage:30h|sex:pooled male and female|tissue:embryo|genotype: / |molecule:mRNA|selection:pA|replicate group:1|replicate:1|BioSampleModel:Model organism or animal | RNAseq Bud13 Bud13 KO 30h | AG01144.2 | AG01144.2 | mRNA | RNA-Seq | TRANSCRIPTOMIC | unspecified | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP129892 | AG01144.2_R1.fastq.gz AG01144.2_R2.fastq.gz | fastq fastq | 12242377920.0 | 80541960.0 | AG01144.2 R1.fastq.gz | 0:76 1:76 | A:3501235324;C:2524126832;G:2520934401;T:3679154562;N:16926801 | 76 | 76 | 3501235324 | 2524126832 | 2520934401 | 3679154562 | 16926801 | SRX3567064 | SRS2838996 | SRA647342 | Yale_Giraldez|Genetics | Yale_Giraldez_Group | 2 | 0.93874 | 0.93814 | 0.2229 | 0.17671 | 0.71102 | 0.71234 | 0.48631 | 0.48352 | 76 | 76 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | United States | 2018-06-23 | Pharyngula | Embryo | Embryo Imprecise | All anatomical structures |