run_metadata: 69442
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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| 69442 | SRR18687235 | SRX14788265 | SRS12547159 | SRP368307 | PRJNA824844 | Single cell analysis of zebrafish marrow in WT and gata2a mutant animals | GSE200503 | Other | Single cell analysis of zebrafish marrow in WT and gata2a mutant animals Overall design: Analysing transcriptomics and chromatin acessability | WT 5mpf scRNA seq | GSM6035263 | source name:wkm|tissue:marrow|age:5mpf|genotype:WT | WT 5mpf scRNA seq | scRNA Seq samples were processed using CellRanger 10x Genomics: v3.1.0 For scATAC Seq peaks were called using MACS2 using the following commands: macs3 callpeak t / MUT1/outs/possorted bam.bam /MUT2/outs/possorted bam.bam / /MUT3/outs/possorted bam.bam n MUT g 1.3E9 and callpeak t / WT1/outs/possorted bam.bam /WT2/outs/possorted bam.bam / /WT3/outs/possorted bam.bam n WT g 1.3E9. Peaks were filtered for qValue < 0.01 and signalValue >2. Analysis was completed using CellRanger ATAC 10x Genomics: v1.2.0 and peaks were specified using the output from MACS2 during the cellrnager atac reanalyze step. An overarching WT peak file was use for all WT samples and an overarching MUT peak file was use for all MUT samples Assembly: GRCz11 | wkm | cells were not treated | 10x genomics microfluidics system was used to isolate cells 3’ scRNAseq was completed using Chromium Next GEM single cell 3’ GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina. | all samples were obtained from zebrafish marrow at the indicated timepoints e.g. 12mpf | tissue:marrow|age:5mpf|genotype:WT | GSM6035263 | GSM6035263: WT 5mpf scRNA seq; Danio rerio; RNA Seq | GSM6035263 r1 | GSM6035263 | 1 | 10x genomics microfluidics system was used to isolate cells three prime scRNAseq was completed using Chromium Next GEM single cell three prime GEM library and Gel bead Kit v3.1 10x Genomics and sequenced using a NextSeq 500 Illumina. scATAC assay for transposable accessible chromatin assay Seq was completed using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 Chromium Next GEM Chip H Single Cell Kit and Chromium i7 Multiplex Kit N Set A 10x Genomics. Libraries were sequenced using NextSeq 500 Illumina. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP368307 | loader:fastq load.py | WT_S1_L001_I1_001.fastq.gz WT_S1_L001_R1_001.fastq.gz WT_S1_L001_R2_001.fastq.gz | fastq fastq fastq | 7887658469.0 | 62107547.0 | GSM6035263 r1 | 0:8 1:28 2:91 | A:1686084589;C:1207047546;G:1347307215;T:1406353747;N:4993680 | 8 | 28 | 91 | 1686084589 | 1207047546 | 1347307215 | 1406353747 | 4993680 | SRX14788265 | SRS12547159 | SRA1400926 | Institute of Cancer and Genomic Sciences, University of Birminhgam | Institute of Cancer and Genomic Sciences, University of Birminhgam | 1 | 0.93208 | 0.13464 | 0.82885 | 0.5507 | 91 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2022-04-08 | Adult | Adult | Marrow | Renal System |