run_metadata: 29572
This data as json
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| 29572 | SRR27368688 | SRX23045200 | SRS20006219 | SRP480346 | PRJNA1057908 | An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq] | GSE252151 | Transcriptome Analysis | cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types predominantly cardiomyocytes. Therefore cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development as they share a number of physiological features with the human heart during development. Therefore we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes validating these genomic regions as cardiac regulatory elements. We share this comprehensive reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells n=3 biological replicates and GFP negative cells 500 000 cells n=3 biological replicates were collected and RNA sequencing was performed on these samples. | parent bioproject:PRJNA1057890 | 30kGFPpos3 Cardiomyocytes | GSM7995230 | source name:Heart|tissue:Heart|cell line:Primary cells|cell type:Cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPpos|treatment:Control|geo loc name:missing|collection date:missing | 30kGFPpos3 Cardiomyocytes | FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin 2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al 2018 using default parameters. There were two sets of counts obtained the first were the reads mapped to genome Zv9 and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9 Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample | Heart | RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols | tissue:Heart|cell line:Primary cells|cell type:Cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPpos|treatment:Control | GSM7995230 | GSM7995230: 30kGFPpos3 Cardiomyocytes; Danio rerio; RNA Seq | GSM7995230 r1 | GSM7995230 | 1 | RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 3000 | SRP480346 | 30kGFPpos3_S39_L008_R1_001.fastq.gz | fastq | 2938808771.0 | 58361915.0 | GSM7995230 r1 | 0:50.35 | A:533261626;C:883704329;G:825929620;T:694986734;N:926462 | 50 | 533261626 | 883704329 | 825929620 | 694986734 | 926462 | SRX23045200 | SRS20006219 | SRA1776396 | Australian Regenerative Medicine Institute, Monash University | Australian Regenerative Medicine Institute, Monash University | 1 | 0.12924 | 0.05415 | 0.92034 | 0.70896 | 51 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Australia | 2023-12-27 | Undetermined | Larval | Heart | Cardiovascular System |