exRNAdisease

Entry Detail

---



General Information

Database ID: exR0089773 RNA Name: hsa-miR-342-3p RNA Type: miRNA Chromosome: chr14 Starnd: + Coordinate: Start Site(bp): 100109715 End Site(bp): 100109737 External Links: hsa-miR-342-3p

Disease Information

Disease Name: Preterm Birth Disease Category: Urogenital Diseases and Pregnancy Complications MeSH ID: D047928 Type: Diseases Category/Female Urogenital Diseases and Pregnancy Complications Alias: Premature Birth//Birth, Premature//Births, Premature//Premature Births//Preterm Birth//Birth, Preterm//Births, Preterm//Preterm Births

Expression Detail

GEO ID: GSE106224 Description: Exosomal RNA may reflect placenta deficiencies and provide better biomarker in preterm birth Experimental Design: Disease vs Control Case Disease Type: Preterm Birth Case Disease SubType: NA Case Sample: Preterm Birth Control Sample: Control Number of Case: 20 Number of Control: 50 Number of Samples: 70

Regulatory Relationship

mRNA targets: Gene Symbol Chromosome Start Site(bp) End Site(bp) Strand AC009133.6 chr16 29812261 29820092 + ACVR1B chr12 51951699 51997078 + CRIM1 chr2 36355778 36551135 + E2F1 chr20 33675477 33686385 - EXOSC6 chr16 70246778 70251940 - IGFBP4 chr17 40443450 40457725 + LASP1 chr17 38869859 38921770 + PAGR1 chr16 29816152 29822489 + UBTF chr17 44205033 44221626 - USP31 chr16 23061406 23149270 - WDR77 chr1 111439890 111449256 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC010327.5 chr19 55216660 55221616 + AC016876.2 chr17 7581964 7584086 - AC021078.1 chr5 149494314 149504670 - AL356488.2 chr1 109100193 109100619 + CKMT2-AS1 chr5 81201341 81301565 - H19 chr11 1995176 2001470 - LINC00894 chrX 149938613 150224580 + NEAT1 chr11 65422774 65445540 + OIP5-AS1 chr15 41283990 41309737 + SNHG20 chr17 77086716 77099902 + SNHG7 chr9 136721366 136728184 - STAG3L5P-PVRIG2P-PILRB chr7 100336104 100367831 + XIST chrX 73820649 73852723 - Display:

Experiment Detail

GEO ID: GSE106224 Sample Source: Blood Source Fraction: Plasma Platform: GPL18573 Method: NGS Num of detected RNA Type: 1 Num of detected RNAs of this Type: 1522 Sample treatment protocol: Whole blood samples were centrifuged for 15 minutes at 2,000×g at 4°C to get plasma. EVs were isolated from 100 ul of plasma using size exclusion columns (iZON qEV, Cambridge MA) with de-gassed 1X PBS from a total of 22 selected samples, 11 from each group (Table 1). Eluate (~500 ul for each fraction) was collected in microfuge tubes individually. The protein contains and concentration for each fraction were assessed by protein gel electrophoresis and Bradford assay (BioRad, Hercules, CA). RNA Extract protocol: RNA was isolated from all plasma samples, the 22 EV samples, and 22 corresponding EV-depleted fractions using miRNeasy Micro Kit (Qiagne, Germantown MD). RNA library preparation protocol: Small RNA sequencing libraries were generated with a modified small RNAseq protocol (manuscript in preparation) that alleviates most of the adapter-miRNA ligation sequence bias problem.

Reference

PMID: 29516617 Title: Extracellular vesicle RNAs reflect placenta dysfunction and are a biomarker source for preterm labour Author: Fallen S, Baxter D, Wu X, Kim TK, Shynlova O, Lee MY, Scherler K, Lye S, Hood L, Wang K Journal: J Cell Mol Med. 2018 May;22(5):2760-2773. Description: We have used an improved small RNA library construction protocol and a newly developed size exclusion chromatography (SEC)-based EV purification method to gain a comprehensive view of circulating RNA in plasma and its distribution by analysing RNAs in whole plasma and EV-associated and EV-depleted plasma.