run_metadata: 34977
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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| 34977 | SRR32588734 | SRX27895217 | SRS24266222 | SRP568323 | PRJNA1232602 | Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains | PRJNA1232602 | Other | In this study Iso Seq was performed on different zebrafish body organs enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues including the brain testis liver eye muscle ovary inner ear and kidney to identify novel isoforms tissue specific transcripts and alternative splicing events. We also made available the Iso Seq data from embryos from different time points hpf 0 6 12 and 24. This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression. | Iso Seq RNA from embryo zero hpf | C2 F2 12 | strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:time 12 hours|dev stage:Embyoys|collection date:2024 06|geo loc name:USA|sex:male|tissue:muscle|BioSampleModel:Model organism or animal | Iso Seq RNA from embyo 12 hpf | C2 F2 12 | C2 F2 12 | The long Read Sequencing libraries was sequenced using PacBio Sequel II | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | PACBIO_SMRT | Sequel II | SRP568323 | m54313U_231111_191642.hifi_reads.flnc.fastq.gz | fastq | 7627931284.0 | 3897936.0 | m54313U 231111 191642.hifi reads.flnc.fastq.gz | 0:1956.92 | A:2146633241;C:1706673950;G:1799625470;T:1974998623;N:0 | 1956 | 2146633241 | 1706673950 | 1799625470 | 1974998623 | 0 | SRX27895217 | SRS24266222 | SRA2089085 | National Human Genome Research Institute|Translational and Functional Genomics Branch | National Human Genome Research Institute National Human Genome Research Institute | T | long read | pacbio | pacbio_modern | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United States | 2025-03-06 | Segmentation | Embryo | Muscle | Muscular System |