run_metadata: 69477
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 69477 | SRR18712326 | SRX14812925 | SRS12569568 | SRP369458 | PRJNA825495 | Regulation of retina microexons by srrm3 in zebrafish | PRJNA825495 | Other | To investigate the role of srrm3 as a regulator of retina microexons RetMICs we have sequenced heads from WT animals at 24 hpf and enucleated eyes from 48 hpf 60 hpf and 72 hpf larvae WT and KO for srrm3. | Eye 48hpf WT b | strain:WT|dev stage:48 hpf|sex:NA|tissue:Eye|BioSampleModel:Model organism or animal | Eyes from 48 hpf larvae WT for the eMIC domain of srrm3. | Eye 48hpf WT | Eye 48hpf WT | WT and srrm3 mutant zebrafish were grown at 28C 14h light/10h dark cycle. Extract protocol: 24 hpf WT fish heads were removed and pulled for RNA extraction using RNA RNeasy Mini kit QIAGEN. Larvae eyes were removed and from twenty to sixty eyes per genotype were pulled for RNA extraction using RNA RNeasy Micro kit QIAGENLibrary preparation: RNA libraries were prepared for sequencing using standard Illumina protocols; polyA selected stranded RNA seq | RNA-Seq | TRANSCRIPTOMIC | RANDOM | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP369458 | Eye_48hpf_WT_b_R1-125.fq.gz Eye_48hpf_WT_b_R2-125.fq.gz | fastq fastq | 15736041750.0 | 62944167.0 | Eye 48hpf WT b R1 125.fq.gz | 0:125 1:125 | A:4076543478;C:3787178416;G:3834447099;T:4028745594;N:9127163 | 125 | 125 | 4076543478 | 3787178416 | 3834447099 | 4028745594 | 9127163 | SRX14812925 | SRS12569568 | SRA1402039 | Centre for Genomic Regulation|Systems Biology | Centre for Genomic Regulation|Systems Biology | 2 | 0.97095 | 0.97209 | 0.05101 | 0.05067 | 0.69408 | 0.69767 | 0.47501 | 0.47714 | 125 | 125 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | random_priming | trueseq | bulk | unknown | unknown | Spain | 2022-04-11 | Hatching | Embryo | Eye | Sensory System |