run_metadata: 39653
This data as json
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| 39653 | SRR2013389 | SRX1021206 | SRS931172 | SRP058095 | PRJNA283297 | Injury activated endocardium plays structural and signalling roles in zebrafish heart regeneration | GSE68650 | Transcriptome Analysis | The zebrafish heart remarkably regenerates post a severe ventricular damage followed by inflammation fibrotic tissue deposition and removal concomitant with cardiac muscle replacement. We have investigated the role of the endocardium in this regeneration process. 3D whole mount imaging in injured hearts revealed that GFP labelled endocardial cells in ET33mi 60A transgenic fish become rapidly activated and highly proliferative at 3 days post cryoinjury dpci. Endocardial cells extensively expand within the injury site and organize to form a coherent structure at 9 dpci that persists throughout the regeneration process. Upon injury endocardial cells strongly up regulate the Notch pathway ligand delta like4 dll4 and the Notch receptors notch1b notch2 and notch3. Expression profiling showed that Notch signalling inhibition affects endocardial gene expression and genes related to extracellular matrix remodelling and inflammation. Gain and loss of function experiments revealed that Notch is required for the organization of the endocardium attenuation of the inflammatory response and cardiomyocyte proliferation. These results demonstrate a novel structural and signalling role for the endocardium during heart regeneration. Overall design: RNA was extracted from apical tip of heart ventricles 72h post cryoinjured adult zebrafish heart treated with DMSO Controls or RO gamma secretase inhibitor at 24 and xxx post injury. | pubmed:28242613 | DMSO Control 3 | GSM1678059 | source name:apex of 3 hearts|developmental stage:adult|strain:AB|stress:cryoinjury|treatment:control|tissue:Heart | DMSO Control 3 | Illumina RTA software v 1.13.48.0 Fastq files extracted with CASAVA 1.8 Reads were pre processed with Cutadapt 1.6.1 To remove TruSeq adaptor. Resulting reads were mapped on the zebrafish transcriptome Ensembl gene build GRCZv9.v75; ftp://ftp.ensembl.org/pub/release 75/gtf/danio rerio/Danio rerio.Zv9.75.gtf.gz and gene expression quantified using RSEM v1.2.3 and Bowtie2 v2.0.6. Data were normalized using TMM with the Bioconductor package EdgeR Differential expression were tested using GLM with the Bioconductor package EdgeR Genome build: GRCZv9.v75 Supplementary files format and content: ROvsControl.NormCounts.csv reports TMM normalized counts per million reads sequenced | apex of 3 hearts | Adult fish were injected with peritoneal RO or DMSO carrier 24h and 48h post cryoinjury of the heart | Total RNA was extracted using Trizol Invitrogen And then purified on Rneasy spin columns Qiagen. RNA integrity RNA Integrity Score ≥ 7.9 And quantity were determined on the Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using TruSeq RNA Sample Preparation Kit v2 standard Illumina protocols | Standard protocols were used to maintain the zebrafish to maturity | developmental stage:adult|strain:AB|stress:cryoinjury|treatment:control|tissue:Heart | GSM1678059 | GSM1678059: DMSO Control 3; Danio rerio; RNA Seq | GSM1678059 | 1 | Total RNA was extracted using Trizol Invitrogen And then purified on Rneasy spin columns Qiagen. RNA integrity RNA Integrity Score ≥ 7.9 And quantity were determined on the Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using TruSeq RNA Sample Preparation Kit v2 standard Illumina protocols | GEO Accession:GSM1678059 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP058095 | DMSO3__JulianeMunch_RNASeq_TTAGGC_L002_R1_001.fastq.gz | fastq | 335316600.0 | 4470888.0 | GSM1678059 r1 | 0:75 | A:90648552;C:77961611;G:75841369;T:90772355;N:92713 | 75 | 90648552 | 77961611 | 75841369 | 90772355 | 92713 | SRX1021206 | SRS931172 | SRA266952 | GEO | Intercellular Signalling in Cardiovascular Development & Disease, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC). | 1 | 0.92509 | 0.08415 | 0.73434 | 0.49782 | 75 | B | usable mapping rate | illumina | early_illumina | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Spain | 2015-05-07 | Adult | Adult | Heart | Cardiovascular System |