run_metadata: 29810
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 29810 | SRR27450809 | SRX23122486 | SRS20076036 | SRP482328 | PRJNA1061565 | Akt is the main kinase mediating the embryonic specification of artery cells | GSE252648 | Transcriptome Analysis | This study aimed at understanding the function of Akt signaling in vascular development in Zebrafish. Overall design: This study used Zebrafish endothelial cells sorted from WT and akt full mutant embryos at 24hpf. Endothelial cells were sorted via the use of transgenic line kdrl:mCherry+. Only mCherry+ were sequenced. So here you can find sample WT and sample akt mutant. | pubmed:39101673 | Zebrafish EC 24hpf WT | GSM8004754 | source name:FAC sorted cells|tissue:FAC sorted cells|cell line:kdrl:mCherry+|cell type:Endothelial Cells|genotype:WT|geo loc name:missing|collection date:missing | Zebrafish EC 24hpf WT | 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 Supplementary files format and content: Tab separated values files and matrix files Assembly: Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: 3 files of barcodes features and matrix | FAC sorted cells | No treatments | Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ 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 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics | Normal zebrafish growth condition | tissue:FAC sorted cells|cell line:kdrl:mCherry+|cell type:Endothelial Cells|genotype:WT | GSM8004754 | GSM8004754: Zebrafish EC 24hpf WT; Danio rerio; RNA Seq | GSM8004754 r1 | GSM8004754 | 1 | Wild type aktmutant Tgkdrl:mCherry tissue were dissected at 24 hpf. Dissected tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ 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 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell 10x genomics | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP482328 | loader:fastq load.py | wt1-23-19_DRT_S1_L001_I1_001.fastq.gz wt1-23-19_DRT_S1_L001_R1_001.fastq.gz wt1-23-19_DRT_S1_L001_R2_001.fastq.gz | fastq fastq fastq | 22261273232.0 | 175285616.0 | GSM8004754 r1 | 0:8 1:28 2:91 | A:4475749188;C:3578353646;G:3836029871;T:4055646794;N:5211557 | 8 | 28 | 91 | 4475749188 | 3578353646 | 3836029871 | 4055646794 | 5211557 | SRX23122486 | SRS20076036 | SRA1780571 | Nicoli lab, School of Medicine, Yale University | Nicoli lab, School of Medicine, Yale University | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2024-01-05 | Pharyngula | Embryo | Multi-tissue | Multi-system |