{"database": "metadata", "table": "run_metadata", "rows": [[56289, "SRR10902599", "SRX7570773", "SRS6006443", "SRP242182", "PRJNA601645", "Identification of TGF b targets in the cardiac outflow tract by transcriptomic analysis", "GSE143770", "Transcriptome Analysis", "Purpose: identifying  with RNA seq  genes targets of Alk5 during the development of the cardiac outflow tract in zebrafish.  Results: we identified several differential expressed genes  with an enrichment in ECM component genes. As a proof of concept  many TGFb known targets also appeared downregulated. Overall design: Zebrafish embryos were treated with Alk5 inhibitor E 616452 or DMSO and hearts were manually extracted at 56 hpf.", null, "pubmed:32990594", null, "Hearts  DMSO 2", "GSM4274434", null, "source name:Hearts|age:56 hpf|genotype:Tgkdrl:eGFP|treatment:DMSO|tissue:Hearts", "Hearts  DMSO 2", "The resulting raw reads were assessed for quality  adapter content and duplication rates with FastQC Reaper version 13 100 was used to trim reads with a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al.  2013.  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 GRCz11.92 using STAR 2.4.0a 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 1.4.5 p1 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 1.18.1Love 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 raw count matrix was batch corrected using CountClust Dey et al.  2017 and then normalized with DESeq2. Genome build: DanRer11 Supplementary files format and content: library size normalized counts", "Hearts", null, "Hearts from 56 hpf Tgkdrl:EGFP control and Alk5 inhibitor treated embryos were manually dissected using forceps.  Approximately 20 hearts per replicate were pooled  and total RNA was isolated using the miRNeasy micro kit Qiagen  combined with on column DNase digestion 100 ng of total RNA was used as input for VAHTS Stranded mRNA seq Library Vazyme preparation  following manufacture\u2019s protocol Vazyme.", null, "age:56 hpf|genotype:Tgkdrl:eGFP|treatment:DMSO|tissue:Hearts", "GSM4274434", "GSM4274434: Hearts  DMSO 2; Danio rerio; RNA Seq", "GSM4274434", null, "1", "Hearts from 56 hpf Tgkdrl:EGFP control and Alk5 inhibitor treated embryos were manually dissected using forceps.  Approximately 20 hearts per replicate were pooled  and total RNA was isolated using the miRNeasy micro kit Qiagen  combined with on column DNase digestion 100 ng of total RNA was used as input for VAHTS Stranded mRNA seq Library Vazyme preparation  following manufacture's protocol Vazyme.", "GEO Accession:GSM4274434", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP242182", null, null, "Giulia_DMSO_2_R1.fastq.gz", "fastq", 2662704304.0, 35727854.0, "GSM4274434 r1", "0:74.53 1:0", "A:669181180;C:594346008;G:625182662;T:773912591;N:81863", 74, 0, null, null, 669181180, 594346008, 625182662, 773912591, 81863, "SRX7570773", "SRS6006443", "SRA1027132", "GEO", "MPI for heart and lung research", 1, 0.93095, null, 0.09862, null, 0.72182, null, 0.4889, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2020-01-16", "Hatching", "Embryo", "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": ["56289"], "units": {}, "query_ms": 14.098662999458611}