run_metadata: 52980
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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| 52980 | SRR9622329 | SRX6385173 | SRS5044691 | SRP212668 | PRJNA551951 | Pre existent adult sox10+ cardiomyocytes contribute to myocardial regeneration in the zebrafish | GSE133571 | Transcriptome Analysis | During heart regeneration in the zebrafish fibrotic tissue is replaced by newly formed cardiomyocytes derived from pre existing ones. It is unclear whether the heart is comprised of several cardiomyocyte populations bearing different capacity to replace lost myocardium. Here using sox10 genetic fate mapping we identified a subset of pre existent cardiomyocytes in the adult zebrafish heart with a distinct gene expression profile that expanded massively post cryoinjury. Genetic ablation of sox10+ cardiomyocytes severely impaired cardiac regeneration revealing that they play a crucial role for heart regeneration. Overall design: Adult zebrafish heart tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR were disassociated and 20 CMs were FAC sorted in single tubes for DESeq2 Library preparation | pubmed:31644901 | CoBFP257 | GSM3912424 | source name:Adult zebrafish heart Uninjured BFP|strain:tgsox10:CreERT2; vmhcl:loxP tagBFP loxP mCherry NTR|condition:Uninjured|tissue:Adult zebrafish heart|sorted cell population:BFP | CoBFP257 | FASTQ files were checked for quality control metrics using FastQC version 0.11.5 and RSeqQC version 2.6.4 Post Quality control raw reads were mapped to the reference genome using Hisat2 version 2.1.0 proceeded by exon counting using featureCounts version 1.6.0 Genome build: Ensembl GRCz11 build 94 Supplementary files format and content: Tab delimeted files containing the Ensembl gene id and the RLE normalized counts | Adult zebrafish heart Uninjured BFP | 0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 | strain:tgsox10:CreERT2;vmhcl:loxP tagBFP loxP mCherry NTR|condition:Uninjured|tissue:Adult zebrafish heart|sorted cell population:BFP | GSM3912424 | GSM3912424: CoBFP257; Danio rerio; RNA Seq | GSM3912424 | 1 | 0.2% RNase inhibitor in Triton X 100 plus Dilute the oligo dT30VN primer to 10 µM by adding 10 µl of 100 µM oligo dT primers and 90 µl of nuclease free water to a tube and mix well. Cells were isolated in the lowest possible volume possibly 0.3 ul of lysis buffer in 0.2 ml PCR tube containing 2 ul of cell lysis buffer 1 ul of oligo dT primeres and dNTP mix. Smart seq2 Picelli S. et al. Nature Protocols 2014 Smart seq2 Picelli S. et al. Nature Protocols 2014 | GEO Accession:GSM3912424 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 3000 | SRP212668 | HVJ22BGX5_sox10_18s002081-1-1_Sande_lane1257.fastq.gz | fastq | 968650125.0 | 12915335.0 | GSM3912424 r1 | 0:75 1:0 | A:245690915;C:241347580;G:238158969;T:243415313;N:37348 | 75 | 0 | 245690915 | 241347580 | 238158969 | 243415313 | 37348 | SRX6385173 | SRS5044691 | SRA915985 | GEO | University of Bern | 1 | 0.92368 | 0.05908 | 0.88316 | 0.56213 | 75 | B | usable mapping rate | illumina | hiseq_era | unknown | poly_a | unknown | sc | single_cell_plate | smartseq | Switzerland | 2019-07-01 | Adult | Adult | Heart | Cardiovascular System |