run_metadata: 42162
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 42162 | SRR5443669 | SRX2733015 | SRS2120913 | SRP103805 | PRJNA382558 | mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish. | GSE97649 | Transcriptome Analysis | 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant | pubmed:26253536 | 48hpf zebrafish FAC sorted endothelial cell wt 1 | GSM2574368 | tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:wildtype | 48hpf zebrafish FAC sorted endothelial cell wt 1 | adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample | purified endothelial cell | 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols | transgene:kdrl eGFP|genotype:wildtype | GSM2574368 | GSM2574368: 48hpf zebrafish FAC sorted endothelial cell wt 1; Danio rerio; RNA Seq | GSM2574368 | 1 | 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols | GEO Accession:GSM2574368 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP103805 | S1_S1_L002_R1_001.fastq.gz | fastq | 1073108602.0 | 14221959.0 | GSM2574368 r2 | 0:75.45 1:0 | A:261964537;C:270187564;G:253958473;T:286941827;N:56201 | 75 | 0 | 261964537 | 270187564 | 253958473 | 286941827 | 56201 | SRX2733015 | SRS2120913 | SRA553927 | GEO | Australian Institute for Bioengineering and Nanotechnology | 1 | 0.93746 | 0.05835 | 0.73734 | 0.50609 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Australia | 2017-04-11 | Hatching | Embryo | Endothelium | Cardiovascular System |