run_metadata: 11815
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 11815 | ERR11799086 | ERX11197445 | ERS16222830 | ERP149963 | PRJEB64798 | Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines | E-MTAB-13228 | Transcriptome Analysis | We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells. | ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25 | Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set | Sample 4 | SAMEA114237385 | Universite Libre de Bruxelles | ENA FIRST PUBLIC:2023 12 25T01:15:27Z|ENA LAST UPDATE:2023 12 25T01:15:27Z|External Id:SAMEA114237385|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:27Z|INSDC last update:2023 12 25T01:15:27Z|INSDC status:public|Submitter Id:E MTAB 13228:Sample 4|age:6|broker name:ArrayExpress|cell type:microglial cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:brain|sample name:E MTAB 13228:Sample 4|scientific name:Danio rerio|sex:male and female|strain:AB | Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines | E MTAB 13228:Sample 4 p | Sample 4 p | Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines | FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set | RNA-Seq | TRANSCRIPTOMIC | Inverse rRNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP149963 | Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines | ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25 | so_zf94_VW4_MDMG7_CD45lo_mhc2dab_MGA_S58_R1.fq.gz so_zf94_VW4_MDMG7_CD45lo_mhc2dab_MGA_S58_R2.fq.gz | fastq fastq | 19305011730.0 | 95569365.0 | E MTAB 13228:so zf94 VW4 MDMG7 CD45lo mhc2dab MGA S58 R | 0:101 1:101 | A:6768262250;C:3044091042;G:2847188942;T:6645295452;N:174044 | 101 | 101 | 6768262250 | 3044091042 | 2847188942 | 6645295452 | 174044 | ERX11197445 | ERS16222830 | ERA26360556 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | 2 | 0.57007 | 0.5231 | 0.45597 | 0.40582 | 0.91579 | 0.91674 | 0.58257 | 0.5625 | 101 | 101 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | rrna_depletion | unknown | bulk | bulk | bulk | United Kingdom | 2023-12-25 | Adult | Adult | Brain | Nervous System |