run_metadata: 56284
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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| 56284 | SRR10899960 | SRX7568764 | SRS6004889 | SRP242096 | PRJNA601476 | Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle | GSE143750 | Transcriptome Analysis | An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line in which the Gal4 transcriptional activator is integrated into the etv2 gene locus. Unexpectedly a cell population with a skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Overall design: GFP+ cells FACS sorted from etv2^ci32Gt; UAS:GFP embryos at 20ss were analyzed using 10X single cell RNA seq | 10X Etv2 homozygous 20ss | GSM4273675 | tissue:FACS sorted GFP+ endothelial cells|age:20 somite stage|cell type:FACS sorted GFP+ endothelial cells|genotype:Etv2 homozygous | 10X Etv2 homozygous 20ss | All processing was performed in 10X Genomics CellRanger v2.0.2 using default parameters Raw basecall files were assembled into fastq files using 'mkfastq' function The 'count' function was used to align Fastq files to zebrafish genome v.9 and to obtain the gene expression matrices Genome build: GRCz10 Supplementary files format and content: mtx matrix files | FACS sorted GFP+ endothelial cells | Whole zebrafish embryos at 20ss were dissociated into a single cell suspension. GFP+ endothelial cells were sorted by FACS.Single cell suspensions were processed through Chromium 10X to generate single cell cDNA libraries attached to microbeads Microbeads were counted and amplified by PCR and the three prime end of the cDNA prepared for sequencing using a modified Nextera XT protocol | age:20 somite stage|cell type:FACS sorted GFP+ endothelial cells|genotype:Etv2 homozygous | GSM4273675 | GSM4273675: 10X Etv2 homozygous 20ss; Danio rerio; RNA Seq | GSM4273675 | 1 | Whole zebrafish embryos at 20ss were dissociated into a single cell suspension. GFP+ endothelial cells were sorted by FACS.Single cell suspensions were processed through Chromium 10X to generate single cell cDNA libraries attached to microbeads Microbeads were counted and amplified by PCR and the three prime end of the cDNA prepared for sequencing using a modified Nextera XT protocol | GEO Accession:GSM4273675 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP242096 | loader:fastq load.py|options: readTypes=TTB read1PairFiles=10X Homo S1 L002 I1 001.fastq.gz read2PairFiles=10X Homo S1 L002 R1 001.fastq.gz read3PairFiles=10X Homo S1 L002 R2 001.fastq.gz | 10X_Homo_S1_L002_R2_001.fastq.gz 10X_Homo_S1_L002_R1_001.fastq.gz 10X_Homo_S1_L002_I1_001.fastq.gz | fastq fastq fastq | 14672202090.0 | 80616495.0 | GSM4273675 r2 | 0:8 1:27 2:147 | A:4504330378;C:3047430997;G:3252225360;T:3865730356;N:2484999 | 8 | 27 | 147 | 4504330378 | 3047430997 | 3252225360 | 3865730356 | 2484999 | SRX7568764 | SRS6004889 | SRA1026915 | GEO | Cincinnati Children's Hospital | 1 | 0.85397 | 0.08065 | 0.85362 | 0.47925 | 147 | B | usable mapping rate | illumina | hiseq_era | 3prime | cdna_unspecified | nextera | sc | single_cell_droplet | 10x | United States | 2020-01-15 | Segmentation | Embryo | Endothelium | Cardiovascular System |