run_metadata: 73968
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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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| 73968 | SRR23291011 | SRX19234271 | SRS16638729 | SRP420309 | PRJNA929990 | Interplay between calcium cycling and sarcomeres directs cardiomyocyte redifferentiation and maturation during regeneration | GSE224156 | Other | Zebrafish hearts can regenerate by replacing damaged tissue with new cardiomyocytes. Although the steps leading up to the proliferation of surviving cardiomyocytes have been extensively studied little is known about the mechanisms that control proliferation and redifferentiation to a mature state. We found that the cardiac dyad a structure that regulates calcium handling and excitation contraction coupling played a key role in the redifferentiation process. A component of the cardiac dyad called leucine rich repeat–containing 10 Lrrc10 acted as a negative regulator of proliferation prevented cardiomegaly and induced redifferentiation. We found that its function was conserved in mammalian cardiomyocytes. This study highlights the importance of the underlying mechanisms required for heart regeneration and their application to the generation of fully functional cardiomyocytes. Overall design: Samples 1 6: Border zone zebrafish cardiomyocytes were FACS sorted based on nppa:mCitrine levels at 7 and 21 post cardiac injury to identify transcriptomic changes over time. Sample 7: iPS CMs from two separate culture plates were transfected with a LRRC10 mCherry fusion construct and sequenced independent of fluorescence where untransfected cells function as an internal control. | pubmed:37200435 | zfCM 7dpi 2 | GSM7016811 | source name:Heart|tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi|geo loc name:missing|collection date:missing | zfCM 7dpi 2 | Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al. 2016 In brief read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file "cel seq2 barcodes.csv" well numbers refer to the 384 well plate in the following ordre: A1 to A24 B1 to B24 and so on until P24. Read 1 was not used for quantification. Read 2 containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Assembly: danRer11 in combination with zebrafish lawson V4.3.2 transcriptome annotation Supplementary files format and content: tab separated count matrices containg spliced unspliced or total reads. | Heart | Zebrafish hearts were cryoinjured 7 or 21 day prior to extraction in extraction buffer. | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. | tissue:Heart|cell line:NA|cell type:cardiomyocyte|genotype:Tgnppa:mCitrine|treatment:7dpi | GSM7016811 | GSM7016811: zfCM 7dpi 2; Danio rerio; RNA Seq | GSM7016811 r1 | GSM7016811 | 1 | Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates each well containing 1 cell containing Vapor Lock oil with CEL Seq2 barcoded primers spike in mRNA and dNTPs Single Cell Discoveries. Plates were spun down and frozen at 80oC until ready for library prep. Plates were processed by Single Cell Discoveries using the SORT seq protocol. In this protocol the CEL seq2 protocol is carried out with the aid of robotic liquid handlers. Illumina sequencing libraries were prepared with the TruSeq small RNA primers Illumina and paired end sequenced at 75 bp read length on the Illumina NextSeq platform. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP420309 | HUB-DB-005_HNWVVBGX9_S4_L002_R1_001.fastq.gz HUB-DB-005_HNWVVBGX9_S4_L002_R2_001.fastq.gz | fastq fastq | 874594286.0 | 10169701.0 | GSM7016811 r2 | 0:26 1:60 | A:227213153;C:160851586;G:182364146;T:303951184;N:214217 | 26 | 60 | 227213153 | 160851586 | 182364146 | 303951184 | 214217 | SRX19234271 | SRS16638729 | SRA1583767 | Jeroen Bakkers, Hubrecht Institute | Jeroen Bakkers, Hubrecht Institute | 2 | 0.11066 | 0.80318 | 0.10409 | 0.40131 | 0.99289 | 0.9333 | 0.66859 | 0.40896 | 26 | 60 | T | B | sc-like readlen | illumina | nextseq | unknown | poly_a | trueseq | sc | single_cell_plate | celseq | Netherlands | 2023-01-31 | Undetermined | Undetermined | Heart | Cardiovascular System |