run_metadata: 51054
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 51054 | SRR8456906 | SRX5263562 | SRS4264367 | SRP180299 | PRJNA515911 | Examination of gene expression in beta cells isolated from either wildtype or alms1 mutant zebrafish | GSE125354 | Transcriptome Analysis | Examination of gene expression in beta cells isolated from either wildtype or alms1 mutant zebrafish Overall design: RNA seq of beta cells isolated from either wildtype or alms1 mutant zebrafish | pubmed:31324766 | WT 1 | GSM3569386 | tissue:beta cells|cell marker:FACS isolated mCherry+ cells|cell type:beta cell enriched|genotype:wildtype|age:5 dpf | WT 1 | trimmed to remove low quality bases at ends mapping to ref genome using CLC Genomics Workbench v 10.0.1 calculated total gene hit counts and RPKM values Genome build: GRCz10 Supplementary files format and content: tab delineated text files of gene expression for each sample set | beta cells | single cell dissociation of whole embryo and FACS sort for mCherry fluorescence Hostelley et al. 2017 Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices. | 5 dpf zebrafish animals of either Tgins:mCherry or alms1 mutants carrying Tgins:mCherry | cell marker:FACS isolated mCherry+ cells|cell type:beta cell enriched|genotype:wildtype|age:5 dpf | GSM3569386 | GSM3569386: WT 1; Danio rerio; RNA Seq | GSM3569386 | 1 | single cell dissociation of whole embryo and FACS sort for mCherry fluorescence Hostelley et al. 2017 Nextera XT transposome with adapters is combined with template DNA. B. Tagmentation to fragment and add adapters. C. Limited cycle PCR to add sequencing primers and indices. | GEO Accession:GSM3569386 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP180299 | WT-1_S201_R1_001.fastq.gz WT-1_S201_R2_001.fastq.gz | fastq fastq | 35627069558.0 | 117970429.0 | GSM3569386 r1 | 0:151 1:151 | A:9789934413;C:8039430934;G:7849037733;T:9945758380;N:2908098 | 151 | 151 | 9789934413 | 8039430934 | 7849037733 | 9945758380 | 2908098 | SRX5263562 | SRS4264367 | SRA836454 | GEO | Medicine, University of Maryland School of Medicine | 2 | 0.91881 | 0.91874 | 0.23468 | 0.24084 | 0.66616 | 0.67969 | 0.46826 | 0.46848 | 151 | 151 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | nextera | bulk | unknown | unknown | United States | 2019-01-18 | Larval | Larval | Pancreas | Endocrine System |