Cardiac Secretome
Background: Exosomes and other extracellular vesicles released from the heart have drawn recent interest for their potential function in paracrine communications and regenerative therapies. This dataset contains the RNA-seq abundance of secreted the exosomal small RNAs including microRNA and piwi-interacting RNAs released from human induced pluripotent stem cells (hiPSCs) as well as hiPSC-derived cardiac cell types (cardiomyocytes, endothelial cells, and fibroblasts).
Methods
Human induced pluripotent stem cell lines from two healthy donor lines were reprogrammed at the Stanford Cardiovascular Institute (Wu et al. 2019). Human iPSCs at or above 20 passages were differentiated into cardiomyocytes (Burridge et al. 2014), endothelial cells (Paik et al. 2018), and cardiac fibroblasts (Zhang et al. 2019) using previously published protocols.
Cell culture media were collected every 48 hours at up to 10 mL from six-well-plate wells of 1 million cells each. The collected culture medium was processed by centrifugation to remove cell debris, after which exosomes were extracted using precipitation or a mechanical based filtration device (Liu et al. 2017).
Exosomal RNAs were extracted using the Qiagen miRNeasy kit. Sequencing library was generated using Illumina TruSeq small RNA kit and were sequenced with 75-nt single -end read on an Illumina NextSeq platform. Small RNA sequencing reads were mapped against GRCh38 human reference genome using STAR v.2.7.3b (Dobin and Gingeras 2016). Minimum match length is 16 and the Illumina TruSeq small RNA library 3p extension adapter is clipped. The output SAM files were converted into sorted BAM using samtools v.1.10 (Li et al. 2009) following removal of reads that are trimmed by STAR at the 5′ end. Aligned reads were assembled using StringTie v.2.1.1 (Kovaka et al. 2019) with the options {-e -b}.
Genome coordinates and annotations of miRNAs were based on miRBase v.22.1 (Kozomara et al. 2019) GFF3 coordinates. Annotations of piRNAs were based on piRNAdb v.1.7.6. Tissue distribution figures were generated with the aid of gganatogram (Maag 2018).
Coming soon.
At a Glance
120
Number of miRNAs
216
Number of piRNAs
12
Number of Samples
Frequently Asked Questions
In the small RNA dataset, we consider a molecule to be secreted at an appreciable level if the average quantile-normalized read counts in both biological replicates are 10 or above. For a secreted molecule to be considered enriched in a cell type, it must also have 5-fold or higher read counts in a single tested cell type compared to the other three cell types in the experiment.
To determine tissue expression patterns, we considered the median total/intracellular miRNA levels in 17 human tissues (spleen, myocardium, small intestine, stomach, bone, brain cerebral cortex frontal, brain cerebellum, liver, gallbladder, bladder, lung, testis, colon, muscle, pancreas, esophagus, prostate, thyroid) using a previously published dataset on human miRNA tissue distributions (Ludwig et al. 2016).
We currently have data from miRNA and piRNA from small RNA sequencing. Other data types including exosomal proteins will be added in the future.