run_metadata: 67835
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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| 67835 | SRR17375069 | SRX13549228 | SRS11443002 | SRP352824 | PRJNA793009 | Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches single cells | GSE192740 | Other | Analysis of CITE seq data Nuclei RNA seq data and single cell RNA seq data on CD45+ and CD45 cells isolated from the livers of mice fed a standard diet SD or western diet WD; fat cholesterol and sugar from healthy and steatotic human livers from hamster liver pig liver chicken liver monkey liver and zebrafish liver. We also performed Spatial Transcriptomics analysis on heatlhy mouse livers NAFLD mouse livers healthy human livers and steatotic human livers. Overall design: Single cell RNA Seq = Liver CD45+ and CD45 cells derived from mice fed a standard diet SD or western diet WD; fat cholesterol and sugar. Liver CD45+ and CD45 cells derived from healthy and obese humans. 10 Visium Spatial Seq = mouse StSt liver mouse StSt capsule mouse NAFLD liver human non steatotic liver human steatotic liver | parent bioproject:PRJNA793005 | pubmed:35021063;pubmed:36304458 | Zebrafish 001 Liver mpeg1.1+ cells Zebrafish | GSM5764410 | tissue:Liver|shortfilename:CS128|strain:Tgmpeg1:EGFPgl22|platform:10x Genomics – v3|digestion method:Ex Vivo|number of added abs:0|number of cells:1229 | Zebrafish 001 Liver mpeg1.1+ cells Zebrafish | Raw data bcl files were first demultiplexed using Cell Ranger mkfastq version 3.1.0 or version 3.0.2 Demultiplexed data was then processed using the Cell Ranger count pipeline version 3.1.0 or version 3.0.2. Cite seq samples were mapped against the TotalSeqA whitelist. Genome build: mm10 Mouse hg19 Human GRCz10 Zebrafish MesAur1.0.100 Hamster GRCg6a.96 Chicken Sscrofa11.1.96 Pig or Macaca facicularis 5.0.100 Macaque Supplementary files format and content: h5 or txt files including raw gene – and if present – antibody counts output CellRanger Count Supplementary files format and content: rds file: Seurat object | Liver | All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022. | shortfilename:CS128|strain:Tgmpeg1:EGFPgl22|platform:10x Genomics – v3|digestion method:Ex Vivo|number of added abs:0|number of cells:1229 | GSM5764410 | GSM5764410: Zebrafish 001 Liver mpeg1.1+ cells Zebrafish; Danio rerio; RNA Seq | GSM5764410 | 1 | All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022. | GEO Accession:GSM5764410 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP352824 | CS128_R1.fastq.gz CS128_R2.fastq.gz | fastq fastq | 38316694094.0 | 321989026.0 | GSM5764410 r1 | 0:28 1:91 | A:10814226120;C:8293271134;G:8575797871;T:10621330197;N:12068772 | 28 | 91 | 10814226120 | 8293271134 | 8575797871 | 10621330197 | 12068772 | SRX13549228 | SRS11443002 | SRA1349905 | GEO | VIB Inflammation Research Center, VIB-University of Ghent | 2 | 0.00626 | 0.88237 | 0.00215 | 0.18876 | 0.99249 | 0.83049 | 0.41451 | 0.59559 | 28 | 91 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Belgium | 2021-12-29 | Undetermined | Undetermined | Liver | Liver and Biliary System |