run_metadata: 34079
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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| 34079 | SRR31040134 | SRX26425397 | SRS22944861 | SRP539406 | PRJNA1174776 | cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA seq] | GSE279845 | Transcriptome Analysis | Cardiac regeneration involves interplay of complex interactions between many different cell types including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response myofibril assembly proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this we determined that cited4a a p300/CBP transcriptional co activator is xxx post injury in mature cardiomyocyte population. Moreover loss of cited4a mutants showed increased dedifferentiation proliferation and accelerated heart regeneration. Thus suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa and uninjured controls UI. Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section. | pubmed:39713454 | Cited 3dpa L001 | GSM8581888 | source name:heart|tissue:heart|genotype:pt38a/pt38a|treatment:3 dy post amputation|geo loc name:missing|collection date:missing | Cited 3dpa L001 | Raw FASTQ files were processed and aligned using the Cell Ranger v. 7.0.0 “count” utility with automatic chemistry detection aligning to the Danio reiro genome GRCz11.108. Processed counts were read into R v4.2.0 using the Seurat package v4.3.0. Nuclei were filtered for a minimum of 3 cells and 200 RNA features. Samples were filtered to exclude nuclei with abnormally high mitochondrial gene expression and RNA features to remove potential contamination and/or doublets. Assembly: GRCz11.108 Supplementary files format and content: matrix.mtx.gz Compressed filtered gene count matrix output by Cell Ranger for each cell in the respective sample. Supplementary files format and content: barcodes.tsv.gz Compressed filtered barcode table output by Cell Ranger with barcodes for each cell in the respective sample. Supplementary files format and content: features.tsv.gz Compressed feature table output by Cell Ranger with feature names for the ENSEMBL identifiers in the gene count matrix for the respective sample. | heart | Uninjured control hearts and 3 dy post amputation dpa were extracted washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor PN 1000494. Library was constructed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller. | tissue:heart|genotype:pt38a/pt38a|treatment:3 dy post amputation | GSM8581888 | GSM8581888: Cited 3dpa L001; Danio rerio; RNA Seq | GSM8581888 r1 | GSM8581888 | 1 | Uninjured control hearts and 3 dy post amputation dpa were extracted washed in 1x PBS and and flash frozen in liquid Nitrogen. Nuclei were isolated as described in methods section using the Chromium Nuclei Isolation Kit with RNase Inhibitor PN 1000494. Library was constructed using the Chromium Next GEM Single Cell three prime Reagent Kits v3.1Dual Index according to the manufacturer's protocol and using the 10X Chromium Controller. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP539406 | loader:fastq load.py|options: readTypes=TBTT read1PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L001 R1 001.fastq.gz read2PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L001 R2 001.fastq.gz read3PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L001 I1 001.fastq.gz read4PairFiles=pt38a 3dpa 022323 Tsang GEX LAF4954A25 S4 L001 I2 001.fastq.gz | pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L001_I1_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L001_I2_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L001_R1_001.fastq.gz pt38a_3dpa_022323_Tsang_GEX_LAF4954A25_S4_L001_R2_001.fastq.gz | fastq fastq fastq fastq | 7511701146.0 | 54432617.0 | GSM8581888 r1 | 0:28 1:90 2:10 3:10 | A:1606850913;C:847555151;G:967521409;T:1476987489;N:20568 | 28 | 90 | 10 | 10 | 1606850913 | 847555151 | 967521409 | 1476987489 | 20568 | SRX26425397 | SRS22944861 | SRA1993641 | Cell Biology, University of Pittsburgh | Cell Biology, University of Pittsburgh | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2024-10-18 | Undetermined | Undetermined | Heart | Cardiovascular System |