{"database": "metadata", "table": "run_metadata", "rows": [[64346, "SRR14559686", "SRX10902992", "SRS8995267", "SRP319994", "PRJNA730305", "Identification of Tcf21 downstream genes in the epicardial cells and cardiomyocytes by transcriptomic analysis", "GSE174505", "Transcriptome Analysis", "Purpose: Studying the epicardium myocardium crosstalk in the zebrafish larval heart. To do so  we aimed to identify  with RNA seq  the genes dysregulated following the loss of the epicardial marker gene tcf21 in sorted epicardial cells and cardiomyocytes. Results: We first analyzed the transcriptome of epicardial and myocardial WT cells and identified cell type specific/enriched genes. Then  we identified several differential expressed genes in tcf21 mutants  including several ligand receptor couples known to mediate the epicardium myocardium crosstalk. Overall design: Hearts were manually extracted from 96 hpf Tgmyl7:mcherry  TgBACtcf21:nls EGFP tcf21+/+ and tcf21 /  zebrafish larvae. Hearts were dissociated into single cell suspensions and FACS was performed to sort epicardial and myocardial cells based on the fluorescence signal.", null, "pubmed:36172839", null, "CMs tcf21+/+ 96 hpf [CM WT 2]", "GSM5318590", null, "tissue:Sorted cardiomyocytes|strain:Tgmyl7:mCherry CAAX+ Tgtcf21:nls.EGFP |genotype:tcf21+/+|developmental stage:96 hpf|cell type:Cardiomyocytes", "CMs tcf21+/+ 96 hpf [CM WT 2]", "Trimmomatic version 0.39 was used to trim reads with a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were used in subsequent analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 Ensembl release 99 using STAR 2.7.3a with the parameter \u201coutFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package Liao et al.  2014. Only reads mapping at least partially inside exons were admitted and aggregated per gene  while reads overlapping multiple genes or aligning to multiple regions were excluded from further analyses. Differentially expressed genes were identified using DESeq2 version 1.26.0 Love et al.  2014. To remove a batch effect from the comparison  the replicates were presented to DESeq2 as covariates DMSO 1/Inhib 1 = 1  DMSO 2/Inhib 2 = 2. The Ensembl annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers. Genome build: DanRer11 GRCz11 Supplementary files format and content: counts.matrix.norm anno.txt: Tab delimited text file includes library size normalized counts.", "Sorted cardiomyocytes", null, "Hearts from 96 hpf Tgmyl7:mcherry  TgBACtcf21:nls EGFP tcf21+/+ and tcf21 /  zebrafish larvae were manually dissected using forceps. Hearts were dissociated into single cell suspensions and FACS was performed to sort cardiomyocytes and epicardial cells. Approximately 6000 1000 cells per replicate were used  and total RNA was isolated using the miRNeasy micro kit Qiagen  combined with on column DNase digestion. 4 ng of total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae 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.", null, "strain:Tgmyl7:mCherry CAAX+ Tgtcf21:nls.EGFP |genotype:tcf21+/+|developmental stage:96 hpf|cell type:Cardiomyocytes", "GSM5318590", "GSM5318590: CMs tcf21+/+ 96 hpf [CM WT 2]; Danio rerio; RNA Seq", "GSM5318590", null, "1", "Hearts from 96 hpf Tgmyl7:mcherry  TgBACtcf21:nls EGFP tcf21+/+ and tcf21 /  zebrafish larvae were manually dissected using forceps. Hearts were dissociated into single cell suspensions and FACS was performed to sort cardiomyocytes and epicardial cells. Approximately 6000 1000 cells per replicate were used  and total RNA was isolated using the miRNeasy micro kit Qiagen  combined with on column DNase digestion. 4 ng of total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae 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.", "GEO Accession:GSM5318590", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP319994", null, "loader:fastq load.py", "Giulia_Lib_CM_WT_2_R1.fastq.gz", "fastq", 3581607451.0, 48771940.0, "GSM5318590 r1", "0:73.44", "A:1004228251;C:800307770;G:813640945;T:963417119;N:13366", 73, null, null, null, 1004228251, 800307770, 813640945, 963417119, 13366, "SRX10902992", "SRS8995267", "SRA1232823", "GEO", "MPI for heart and lung research", 1, 0.93484, null, 0.07055, null, 0.82134, null, 0.52578, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2021-05-16", "Larval", "Larval", "Heart", "Cardiovascular System"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["64346"], "units": {}, "query_ms": 7.725411996943876}