run_metadata: 68876
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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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| 68876 | SRR25099321 | SRX20852447 | SRS18129437 | SRP362545 | PRJNA812617 | Sinus venosus adaptation models prolonged cardiovascular disease and reveals insights into evolutionary transitions of the vertebrate heart | GSE195548 | Transcriptome Analysis | How two chambered hearts in basal vertebrates have evolved from single chamber hearts found in ancestral chordates remains unclear. Here we show that the teleost sinus venosus SV is a chamber like vessel comprised of an outer layer of smooth muscle cells. We find that in adult zebrafish nr2f1a mutants which lack atria the SV comes to physically resemble the thicker bulbus arteriosus BA at the arterial pole of the heart through an adaptive hypertensive response involving smooth muscle proliferation due to aberrant hemodynamic flow. Single cell transcriptomics show that smooth muscle and endothelial cell populations within the adapting SV also take on arterial signatures. Bulk transcriptomics of the blood sinuses flanking the tunicate heart reinforce a model of greater equivalency in ancestral chordate BA and SV precursors. Our data simultaneously reveal that secondary complications from congenital heart defects can develop in adult zebrafish similar to those in humans and that the foundation of equivalency between flanking auxiliary vessels may remain latent within basal vertebrate hearts. Overall design: RNA seq of zebrafish heart chambers | parent bioproject:PRJNA804024 | pubmed:37679366 | aco mutant ventricle 2 | GSM7524718 | source name:isolated WT ventricle|tissue:isolated WT ventricle|cell type:mixed|genotype:aco AB/TU|treatment:adult 6 month 1.5 years|geo loc name:missing|collection date:missing | aco mutant ventricle 2 | Zebrafish RNA seq reads were aligned to the UCSC zebrafish genome danRer11 using STAR aligner post trimming the Illumina adapter using cutadapt These libraries were prepped across multiple batches with different library types in terms of RNA strand and sequencing mode single end or paired end. Therefore we treated them as single end libraries by choosing read1 or read2 to match the strand as much as possible and batch correction was applied as described below. Only uniquely aligned reads were retained for downstream analysis. Gene expression levels were quantified as raw read counts using FeatureCounts in the subread package with an option “ O fracOverlap 0.8” and with a proper strand option s. Given the mixed sequencing batches and library types we incorporated RUVseq batch correction RUVs k=1 in DESeq2 differential analysis. Differentially expressed genes were identified by FDR < 0.05. Hierarchical clustering was performed using the Pearson correlation coefficient as a similarity measure under Ward’s criterion and a heatmap was visualized in z score. Assembly: GRCz10/danRer10 Supplementary files format and content: text of DESeq2 data with LogFC P value FDR normalized expression and raw counts | isolated WT ventricle | The heart chambers bulbous arteriosus and sinus venosus were removed from the adult fish and then separated into their respective tissues. Heart tissues from 20 fish were pooled and then placed in TRIZOL. RNA was harvested using phenol chloroform separation and a PureLink RNA Micro Kit Invitrogen. The RNA was submitted to the CCHMC core for library generation and sequencing. Singles and paired end sequencing was performed. RNA libraries prepared for sequencing using standard protocols | tissue:isolated WT ventricle|cell type:mixed|genotype:aco AB/TU|treatment:adult 6 month 1.5 years | GSM7524718 | GSM7524718: aco mutant ventricle 2; Danio rerio; RNA Seq | GSM7524718 r1 | GSM7524718 | 1 | The heart chambers bulbous arteriosus and sinus venosus were removed from the adult fish and then separated into their respective tissues. Heart tissues from 20 fish were pooled and then placed in TRIZOL. RNA was harvested using phenol chloroform separation and a PureLink RNA Micro Kit Invitrogen. The RNA was submitted to the CCHMC core for library generation and sequencing. Singles and paired end sequencing was performed. RNA libraries prepared for sequencing using standard protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP362545 | loader:fastq load.py | aco_SV_rd2_2.fastq.gz | fastq | 2842036273.0 | 28138973.0 | GSM7524718 r1 | 0:101 | A:832566894;C:633773069;G:668950393;T:706598442;N:147475 | 101 | 832566894 | 633773069 | 668950393 | 706598442 | 147475 | SRX20852447 | SRS18129437 | Molecular Cardiovascular Biology Division, Cincinnati Children's Hospital Medical Center | 1 | 0.94423 | 0.11196 | 0.72147 | 0.47741 | 101 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2023-06-30 | Adult | Adult | Heart | Cardiovascular System |