run_metadata: 60874
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| 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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| 60874 | SRR12610268 | SRX9093634 | SRS7339294 | SRP281427 | PRJNA662347 | Cardiomyocyte heterogeneity in zebrafish development and regeneration | GSE157662 | Transcriptome Analysis | Contrary to adult mammals zebrafish are able to regenerate their heart post cardiac injury. This regenerative response relies in part on the endogenous ability of cardiomyocytes CMs to dedifferentiate and proliferate to replenish the lost muscle. However CM heterogeneity and population dynamics during development and regeneration remain poorly understood. Through comparative transcriptomic analyses of the developing and adult zebrafish heart we identified tnnc2 and tnni4b.3 expression as markers for CMs at early and late developmental stages respectively. Using newly developed reporter lines for these genes we investigated their expression dynamics during development and regeneration and observed interesting expression patterns. tnnc2 reporter lines label most CMs at embryonic stages and this labeling declines rapidly during larval stages; in adult hearts expression is only detectable in a subset of CMs. Conversely expression of a tnni4b.3 reporter is initially visible in outer curvature CMs at larval stages and it is subsequently present in a vast majority of the CMs in adult hearts. Interestingly we find that the adult CMs labeled by the embryonic reporter display higher levels of Tgtp1:EGFP expression which indicates active Notch signaling. To further characterize this CM population we performed transcriptomic analysis and found that it expresses genes encoding components of the Notch signaling pathway as well as markers of immature CMs. Moreover during heart regeneration proliferating CMs in the injured area activate the embryonic CM reporter. Overall our findings provide further evidence of cardiomyocyte heterogeneity in the adult zebrafish heart. Overall design: Total RNA was isolated from sorted myl7:EGFP+ 7000 cells and tp1:EGFP+/myl7:DsRed2 NLS+ 2000 cells. In both cases RNA was extracted using RNeasy Micro Kit Qiagen following manufacturer's instructions. | pubmed:33857482 | myl7 1 | GSM4772980 | source name:FACS sorted myl7:EGFP+ zebrafish cardiomyocytes|developmental stage:Adult|cell type:Cardiomyocytes|tissue:Heart|genotype:myl7:EGFP+ | myl7 1 | Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Bolger et al. 2014. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 GRCz11.98 using STAR 2.6.1d with the parameter “ outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al. 2013. The number of reads aligning to genes was counted with FeatureCounts tool from the Subread package 1.6.5 Liao et al. 2014. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Differentially expressed genes were identified using DESeq2 version 1.26.0 Love et al. 2014. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: DanRer11 Supplementary files format and content: counts.matrix.norm anno | FACS sorted myl7:EGFP+ zebrafish cardiomyocytes | For RNA seq RNA was isolated from sorted myl7:EGFP+ and tp1:EGFP+/myl7:DsRed2 NLS+ ventricular zebrafish CMs using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and approximately 1 2ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech and NEXTflexTM Rapid Directional qRNA Seq Kit Bioo Scientific following manufacturers protocol. | developmental stage:Adult|cell type:Cardiomyocytes|tissue:Heart|genotype:myl7:EGFP+ | GSM4772980 | GSM4772980: myl7 1; Danio rerio; RNA Seq | GSM4772980 | 1 | For RNA seq RNA was isolated from sorted myl7:EGFP+ and tp1:EGFP+/myl7:DsRed2 NLS+ ventricular zebrafish CMs using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and approximately 1 2ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech and NEXTflexTM Rapid Directional qRNA Seq Kit Bioo Scientific following manufacturers protocol. | GEO Accession:GSM4772980 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP281427 | Ruben_sample_myl7_1_R1.fastq.gz | fastq | 2949217134.0 | 39569236.0 | GSM4772980 r1 | 0:74.53 1:0 | A:846793773;C:636612082;G:642754162;T:823002049;N:55068 | 74 | 0 | 846793773 | 636612082 | 642754162 | 823002049 | 55068 | SRX9093634 | SRS7339294 | SRA1122721 | GEO | MPI for heart and lung research | 1 | 0.92424 | 0.13815 | 0.84524 | 0.47678 | 75 | B | usable mapping rate | illumina | nextseq | full_length | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | Germany | 2020-09-08 | Adult | Adult | Heart | Cardiovascular System |