run_metadata: 56909
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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| 56909 | SRR11186476 | SRX7806774 | SRS6219809 | SRP250827 | PRJNA608912 | Single cell analysis of non myocytes during heart regeneration reveals sequential coordinated responses from distinct cell populations [scRNA seq] | GSE145980 | Transcriptome Analysis | Cardiac regeneration occurs primarily through proliferation of existing cardiomyocytes yet the regenerative response also involves complex interactions between distinct cardiac cell types including not only cardiomyocytes but also non cardiomyocytes nonCMs. However the molecular features and cellular functions of the highly heterogeneous populations of nonCMs and how these populations cooperate to regenerate the injured heart remain largely unexplored. Using the newly developed LIGER algorithm that allows flexible modeling across highly diverse single cell datasets we analyzed the transcriptome dynamics of 61 977 individual nonCMs isolated at multiple time points during zebrafish heart regeneration. Combining single cell analysis and in situ hybridization we identified major nonCM cell types including multiple novel subpopulations with unique tempo spatial distributions and highly cooperative interactions in the regenerating heart. Interestingly genetic perturbation of macrophage function by kit knockout led to accumulation of fibrotic deposits and severely compromised cardiomyocyte proliferation and myocardium regeneration. Our single cell transcriptomic analysis of nonCMs during cardiac regeneration provides a blueprint for interrogating the molecular and cellular basis of cardiac regeneration. Overall design: Single cell RNA seq profiles of cardiac non cardiomyocytes isolated at multiple time points during zebrafish heart regeneration were generated by deep sequencing using 10X Genomics Chromium System. | parent bioproject:PRJNA608906 | pubmed:34523214 | kit 14dpi 1 | GSM4340649 | source name:kit 7dpi nonCMs|genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:7 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs | kit 14dpi 1 | I1 8 bp sample barcode R1 16 bp feature barcode + 10 bp UMI and R2 reads; Qualities of de barcoded raw sequence reads were checked by fastqc. Raw sequencing data was demultiplexed debarcoded mapped to UCSC DanRer10 genome and counted by UNC TGL bioinformatic staff following the Cell Ranger/2.0.2 pipeline. The Cell Ranger output of collapsed UMI counts were then processed and analyzed in R. Genome build: UCSC DanRer10 Supplementary files format and content: two csv files containing raw count values for each cell in the samples of wild type and kit mutant respectively | kit 7dpi nonCMs | Zebrafish were anesthetized by immersion with 0.04% tricaine and immobilized in a dampened foam with ventral side up. A small incision was made between the gills to expose the ventricle. About 20% of ventricular apex was resected using iridectomy scissors. post apex resection fish were returned to a recovery tank with fresh system water. | Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5. | Zebrafish were raised and maintained under standard laboratory conditions. | genotype/variation:kit mutant; kitaw34b2;kitbsa15356|age:4 month 6 month|treatment/timepoint:7 xxx post injury|tissue:heart|cell type:cardiac non cardiomyocytes nonCMs | GSM4340649 | GSM4340649: kit 14dpi 1; Danio rerio; RNA Seq | GSM4340649 | 1 | Primary cells from zebrafish ventricles subjected to control operation or apex resection were isolated. Cardiomyocytes and non cardiomyocytes were separated by 3 times of centrifugation at 200g for 5 minutes at 4°C. isolated non cardiomyocytes from zebrafish ventricles subjected to control operation or apex resection at indicated time points were loaded into the Chromium controller 10X Genomics and processed with Chromium Single Cell Reagent Kit v2 10X Genomics. Illumina libraries were prepared using NextSeq 500/550 kit v2.5. | GEO Accession:GSM4340649 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP250827 | loader:fastq load.py|options: readTypes=TBB read1PairFiles=kit 14dpi 1 S1 L001 I1 001.fastq.gz read2PairFiles=kit 14dpi 1 S1 L001 R2 001.fastq.gz read3PairFiles=kit 14dpi 1 S1 L001 R1 001.fastq.gz | kit_14dpi_1_S1_L001_I1_001.fastq.gz kit_14dpi_1_S1_L001_R1_001.fastq.gz kit_14dpi_1_S1_L001_R2_001.fastq.gz | fastq fastq fastq | 7722224136.0 | 58501698.0 | GSM4340649 r1 | 0:8 1:98 2:26 | A:2225663837;C:1761078052;G:1766349345;T:1968017965;N:1114937 | 8 | 98 | 26 | 2225663837 | 1761078052 | 1766349345 | 1968017965 | 1114937 | SRX7806774 | SRS6219809 | SRA1048427 | GEO | University of North Carolina at Chapel Hill | 2 | 0.94765 | 0.00393 | 0.05485 | 0.0007 | 0.8801 | 0.99421 | 0.66266 | 0.57166 | 98 | 26 | B | T | sc-like readlen | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2020-02-26 | Adult | Adult | Heart | Cardiovascular System |