run_metadata: 9815
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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| 9815 | ERR3931359 | ERX3938949 | ERS4329526 | ERP120057 | PRJEB36819 | Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga | E-MTAB-8800 | Transcriptome Analysis | Kit ligand Kitlg is a pleiotropic cytokine with a prominent role in vertebrate erythropoiesis. Due to whole genome duplication zebrafish possess two copies of Kit ligand Kitlga and Kitlgb. We generated a recombinant version of Kitlga tested its biological activity in culture of zebrafish kidney marrow cells and performed RNA seq analysis. Using this assay we demonstrate that Kitlga cooperates with other factors to promote erythroid cell expansion ex vivo. | ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05 | Protocols: Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11 1007 1020 doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo dexamethasone Dex or Epo Dex and Kitlga according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number which is regarded as criteria for high quality total RNA ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. | WKM 5 EaD | SAMEA6565183 | Institute of Molecular Genetics of the Czech Academy of Sciences | ENA first public:2021 12 31|ENA last update:2021 12 31|External Id:SAMEA6565183|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 12 31T00:11:11Z|INSDC last update:2021 12 31T00:11:11Z|INSDC status:public|Submitter Id:E MTAB 8800:WKM 5 EaD|broker name:ArrayExpress|cell type:erythroid progenitor cell|common name:zebrafish|developmental stage:adult|disease:normal|genotype:Tg gata1:DsRed|growth condition:Erythropoietin Dexamethas1|individual:WKM5|organism part:head kidney|sample name:E MTAB 8800:WKM 5 EaD | NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga | E MTAB 8800:WKM 5 EaD s | WKM 5 EaD s | Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga | Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11 1007 1020 doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo dexamethasone Dex or Epo Dex and Kitlga according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number which is regarded as criteria for high quality total RNA ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies. | Experimental Factor: stimulus:kit ligand | RNA-Seq | TRANSCRIPTOMIC | Inverse rRNA | SINGLE | ILLUMINA | NextSeq 500 | ERP120057 | NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga | ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05 | 9_WKM_5_EaD.fastq.gz | fastq | 3602342027.0 | 47707938.0 | E MTAB 8800:WKM 5 EaD | 0:75.51 1:0 | A:717278291;C:1084375347;G:1027250408;T:773351695;N:86286 | 75 | 0 | 717278291 | 1084375347 | 1027250408 | 773351695 | 86286 | ERX3938949 | ERS4329526 | ERA2383450 | Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive | Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive | 1 | 0.96461 | 0.20281 | 0.85303 | 0.74553 | 75 | B | usable mapping rate | illumina | nextseq | full_length | rrna_depletion | smarter | bulk | bulk | bulk | Czech Republic | 2021-12-31 | Adult | Adult | Multi-tissue | Multi-system |