run_metadata: 60925
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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| 60925 | SRR12658670 | SRX9139728 | SRS7381394 | SRP282672 | PRJNA663960 | Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development | GSE158099 | Transcriptome Analysis | We used single cell RNA sequencing to investigate the expression and the heterogeneity of wild type and runx1 mutant cd41 GFPLow cd41GFP hematopoietic stem and progenitor cells at embryonic 2.5 dpf dpf and larval stages 6 10 dpf 16 dpf. Overall design: Single cell RNA seq with FACS sorted cd41 GFPlow cells from wild type and runx1 / at 2.5 6 10 dpf 16 dpf. | parent bioproject:PRJNA663961 | pubmed:34492681 | cd41:GFPlow runx1 / 10dpf | GSM4792213 | tissue:sorted cd41:GFPlow|strain:EK|genotype/variation:runx1 / del8 hg96 tgcd41:GFP|age:10 dpf|cell subset:sorted cd41:GFPlow | cd41:GFPlow runx1 / 10dpf | Sequences from the Chromium platform were de multiplexed and aligned using CellRanger ver. 2.0.2 from 10x Genomics using custom zebrafish reference genome GRCz10 and transcript annotation reference GRCz10.87 with default parameters. Genome build: GRCz10 Supplementary files format and content: barcodes.tsv genes.tsv features.tsv matrix.mtx | sorted cd41:GFPlow | Single cell: dissociation protocol: DOI: 10.1016/j.mex.2018.10.009. Single cells were captured using 10x Genomics Chromium. Single cell RNA seq libraries were prepared using Chromium Single Cell 3’ Library & Gel Bead Kit v3. Cell lysis cDNA preparation and library construction were prepared following the manufacturer's protocol. | strain:EK|genotype/variation:runx1 / del8 hg96 tgcd41:GFP|age:10 dpf|cell subset:sorted cd41:GFPlow | GSM4792213 | GSM4792213: cd41:GFPlow runx1 / 10dpf; Danio rerio; RNA Seq | GSM4792213 | 1 | Single cell: dissociation protocol: DOI: 10.1016/j.mex.2018.10.009. Single cells were captured using 10x Genomics Chromium. Single cell RNA seq libraries were prepared using Chromium Single Cell three prime Library & Gel Bead Kit v3. Cell lysis cDNA preparation and library construction were prepared following the manufacturer's protocol. | GEO Accession:GSM4792213 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 550 | SRP282672 | loader:fastq load.py|options: platform=Illumina readTypes=TBT read1PairFiles=SC6.zf rx1 10dpf cd41.R1.fastq.gz read2PairFiles=SC6.zf rx1 10dpf cd41.R2.fastq.gz read3PairFiles=SC6.zf rx1 10dpf cd41.I1.fastq.gz | SC6.zf_rx1_10dpf_cd41.I1.fastq.gz SC6.zf_rx1_10dpf_cd41.R1.fastq.gz SC6.zf_rx1_10dpf_cd41.R2.fastq.gz | fastq fastq fastq | 14974412901.0 | 117908763.0 | GSM4792213 r1 | 0:28 1:91 2:8 | A:3982657699;C:3492784275;G:3627405921;T:3870769189;N:795817 | 28 | 91 | 8 | 3982657699 | 3492784275 | 3627405921 | 3870769189 | 795817 | SRX9139728 | SRS7381394 | SRA1126726 | GEO | NHGRI | 1 | 0.94556 | 0.09828 | 0.81566 | 0.51593 | 91 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2020-09-16 | Larval | Larval | Undetermined | Undetermined |