run_metadata: 70092
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 70092 | SRR24739157 | SRX20516499 | SRS17826365 | SRP377666 | PRJNA843735 | Alpha 1 adrenergic signaling drives cardiac regeneration through activation of extracellular matrix remodeling transcriptional program in macrophages | GSE205103 | Transcriptome Analysis | Autonomic drive plays a pivotal role in cardiac regeneration. Sympathetic or cholinergic denervation impairs myocardial regrowth in neonatal mouse and zebrafish hearts. Here we uncovered the mechanistic underpinning of adrenergic signaling in regenerative repair of the heart to be critically dependent on immunomodulation. Through pharmacological and genetic manipulations we identified adrenergic receptor alpha 1 as a key regulator of macrophage phenotypic diversification following myocardial infarction in zebrafish. Single cell transcriptomics revealed that the receptor signals activation of an 'extracellular matrix remodeling' transcriptional program characterized by upregulation of matrix proteins and matrix modifying enzymes in a macrophage subset. Functionally adrenergic receptor alpha 1 activated macrophages regulate fibrotic response of the heart by mediating collagenous extracellular matrix turnover and myofibroblast activation allowing vascularization and cardiomyocyte cell cycle entry at the infarcted lesion. These findings not only unravel the mechanism of adrenergic signaling in macrophage phenotypic and functional determination but also highlight the potential of neural modulation for regulation of fibrosis and coordination of myocardial regenerative response. Overall design: Zebrafish hearts subjected to cryoinjury were collected at 7 dpi dissociated and live cells sorted by FACS analyzed with scRNAseq | pubmed:37875117 | control heart cryoinjured | GSM7427915 | source name:heart|strain:AB/TU|time:7 xxx post injury|tissue:heart|genotype:TgBACcsf1ra:GAL4 VP16i186; TgUAS:NTR mCherryc264|treatment:cryoinjury|geo loc name:missing|collection date:missing | control heart cryoinjured | the steps until acquiring the fastq files demultiplexing conversion to fastq were done by the Genomics technology platform in Max Delbruck Centrum. Then Cell Ranger software v6.0.1 was used for counting alignment with the fastq files. https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger then Seu Assembly: GRCz11 release 104 Supplementary files format and content: Tab separated values files and matrix files | heart | zebrafish with TgBACcsf1ra:GAL4 VP16i186; TgUAS:NTR mCherryc264 transgenes subjected to cryoinjury and hearts were collected at 7 dpi and transferred into dissociation solution containing 0.26 U/ml LiberaseTM enzyme mixture Sigma and 1X Pluronic F 68 ThermoFisher in HBSS. Hearts were incubated in dissociation solution for 30 minutes with shaking at 750 rpm at 37°C with intermittent pipetting every 5 minutes. Live cells were sorted by FACS. Library was constructed according to the manufacterer’s instructions of Chromium Single Cell three prime Reagent Kits User Guide v3.1 Chemistry. library preparation was done by Genomics technology platform in Max Delbruck Centrum | strain:AB/TU|time:7 xxx post injury|tissue:heart|genotype:TgBACcsf1ra:GAL4 VP16i186; TgUAS:NTR mCherryc264|treatment:cryoinjury | GSM7427915 | GSM7427915: control heart cryoinjured; Danio rerio; RNA Seq | GSM7427915 r1 | GSM7427915 | 1 | zebrafish with TgBACcsf1ra:GAL4 VP16i186; TgUAS:NTR mCherryc264 transgenes subjected to cryoinjury and hearts were collected at 7 dpi and transferred into dissociation solution containing 0.26 U/ml LiberaseTM enzyme mixture Sigma and 1X Pluronic F 68 ThermoFisher in HBSS. Hearts were incubated in dissociation solution for 30 minutes with shaking at 750 rpm at 37°C with intermittent pipetting every 5 minutes. Live cells were sorted by FACS. Library was constructed according to the manufacterer's instructions of Chromium Single Cell three prime Reagent Kits User Guide v3.1 Chemistry. library preparation was done by Genomics technology platform in Max Delbruck Centrum | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP377666 | loader:fastq load.py | P1792_SP106_009_S1_L001_R1_001.fastq.gz P1792_SP106_009_S1_L001_R2_001.fastq.gz | fastq fastq | 44106695018.0 | 373785551.0 | GSM7427915 r1 | 0:28 1:90 | A:11119116130;C:11277976932;G:10463548412;T:11244752649;N:1300895 | 28 | 90 | 11119116130 | 11277976932 | 10463548412 | 11244752649 | 1300895 | SRX20516499 | SRS17826365 | SRA1644267 | Max Delbruck Centrum | Max Delbruck Centrum | 2 | 0.00282 | 0.92876 | 0.0008 | 0.04739 | 0.99669 | 0.89246 | 0.3378 | 0.50554 | 28 | 90 | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Germany | 2023-05-25 | Undetermined | Undetermined | Heart | Cardiovascular System |