run_metadata: 70969
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 70969 | SRR21007397 | SRX17024128 | SRS14609021 | SRP390913 | PRJNA868351 | Hematopoietic stem and progenitor cell heterogeneity is inherited from the embryonic hemogenic endothelium [scRNA seq] | GSE210941 | Transcriptome Analysis | Investigate the role of miR128 in the EHT process and the formation of nHSPCs Overall design: Comparative gene expression analysis of RNA seq data for WT and MT samples for miRNA128 in Human and Fish | parent bioproject:PRJNA868347 | pubmed:37460694 | gRNA csnk1 26HPF scRNAseq | GSM6443155 | source name:trunk tissue containing the AGM|cell type:Endothelial Cells|tissue:trunk tissue containing the AGM|strain:Tgkdrl:GFP zn1|age:26HPF|geo loc name:missing|collection date:missing | gRNA csnk1 26HPF scRNAseq | The barcoded processing gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: Tab separated values files and matrix files | trunk tissue containing the AGM | Wild type miR 128Δ/Δ csnk1a1 and jag1b g3’UTR mutants Tgkdrl:GFP zn1 trunk tissue containing the AGM were dissected at 26 hpf. Dissected trunk tissues were dissociated into single cell suspensions and subjected to FACS. GFP+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions | cell type:Endothelial Cells|tissue:trunk tissue containing the AGM|strain:Tgkdrl:GFP zn1|age:26HPF | GSM6443155 | GSM6443155: gRNA csnk1 26HPF scRNAseq; Danio rerio; RNA Seq | GSM6443155 r1 | GSM6443155 | 1 | Wild type miR 128Δ/Δ csnk1a1 and jag1b gthree primeUTR mutants Tgkdrl:GFP zn1 trunk tissue containing the AGM were dissected at 26 hpf. Dissected trunk tissues were dissociated into single cell suspensions and subjected to FACS. GFP+ cells which had 85% cell viability were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP390913 | loader:fastq load.py|options: readTypes=TBB read1PairFiles=csnk1a DRT S2 L003 I1 001.fastq.gz read2PairFiles=csnk1a DRT S2 L003 R1 001.fastq.gz read3PairFiles=csnk1a DRT S2 L003 R2 001.fastq.gz | csnk1a_DRT_S2_L003_I1_001.fastq.gz csnk1a_DRT_S2_L003_R1_001.fastq.gz csnk1a_DRT_S2_L003_R2_001.fastq.gz | fastq fastq fastq | 17585727973.0 | 138470299.0 | GSM6443155 r1 | 0:8 1:28 2:91 | A:4685099762;C:3662694223;G:3795199750;T:4334481609;N:490237 | 8 | 28 | 91 | 4685099762 | 3662694223 | 3795199750 | 4334481609 | 490237 | SRX17024128 | SRS14609021 | SRA1473366 | Nicoli Lab, Genetics/Internal Medicine, Yale University | Nicoli Lab, Genetics/Internal Medicine, Yale University | 2 | 0.01126 | 0.9112 | 0.00402 | 0.18979 | 0.98137 | 0.7838 | 0.32952 | 0.50602 | 28 | 91 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2022-08-10 | Pharyngula | Embryo | Trunk | Surface Structure |