exRNAdisease

Entry Detail

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General Information

Database ID: exR0000257 RNA Name: ADAMTS19 RNA Type: mRNA Chromosome: chr5 Starnd: + Coordinate: Start Site(bp): 129460281 End Site(bp): 129738683 External Links: ENSG00000145808

Disease Information

Disease Name: Down Syndrome Disease Category: Congenital, Hereditary, and Neonatal Diseases and Abnormalities MeSH ID: D004314 Type: Diseases Category/Congenital, Hereditary, and Neonatal Diseases and Abnormalities Alias: Syndrome, Down//Mongolism//47,XY,+21//Trisomy G//47,XX,+21//Down's Syndrome//Downs Syndrome//Syndrome, Down's//Trisomy 21//Trisomy 21, Mitotic Nondisjunction//Down Syndrome, Partial Trisomy 21//Partial Trisomy 21 Down Syndrome//Trisomy 21, Meiotic Nondisjunction

Expression Detail

GEO ID: GSE16176 Description: Expression profiles of amniotic fluid from human fetuses with Down syndrome and euploid controls Experimental Design: Disease vs Control Case Disease Type: Down Syndrome Case Disease SubType: NA Case Sample: Down Syndrome Control Sample: Normal Number of Case: 7 Number of Control: 7 Number of Samples: 14

Regulatory Relationship

mRNA targets: Gene Symbol Chromosome Start Site(bp) End Site(bp) Strand RIT1 chr1 155897808 155911404 - NSFL1C chr20 1442162 1473842 - SCFD2 chr4 52872982 53366066 - RPL23A chr17 28719985 28724359 + TPT1 chr13 45333471 45341370 - GRK5 chr10 119207571 119459745 + GPR137C chr14 52552836 52637713 + SMPD2 chr6 109440724 109443919 + FAM124A chr13 51222334 51284241 + TSPAN6 chrX 100627108 100639991 - ZNF614 chr19 52012765 52030240 - EIF2D chr1 206571292 206612465 - GATA5 chr20 62463497 62475995 - CCZ1 chr7 5898725 5926550 + BZW1 chr2 200810594 200827338 + RPL3 chr22 39312882 39320389 - SYPL1 chr7 106090503 106112576 - BTAF1 chr10 91923770 92030325 + XPO6 chr16 28097979 28211920 - STX8 chr17 9250471 9576591 - HNRNPH3 chr10 68331174 68343191 + KHDRBS1 chr1 32013868 32060850 + RARB chr3 25174332 25597932 + FBXL19 chr16 30923055 30948783 + TPR chr1 186311652 186375693 - ATXN10 chr22 45671798 45845307 + SLC38A1 chr12 46183063 46270017 - NRAS chr1 114704469 114716771 - FLNA chrX 154348524 154374638 - DDOST chr1 20651767 20661544 - miRNA targets: NA circRNA targets: NA lncRNA targets: NA Display:

Experiment Detail

GEO ID: GSE16176 Sample Source: Amniotic Fluid Source Fraction: Supernatant Platform: GPL570 Method: Microarray Num of detected RNA Type: 1 Num of detected RNAs of this Type: 17063 Sample treatment protocol: NA RNA Extract protocol: RNA was extracted from 10 mL AF with 30 mL TRIzol LS Reagent (Invitrogen, Carlsbad, CA) and 8 mL chloroform. After RNA extraction, RNA was purified and DNA was removed using the RNeasy® Maxi Kit, including the DNase step according to the manufacturer's protocol (QIAGEN, Valencia, CA). RNA was precipitated using 3M NaOAc and 100% ethanol, and 80% ethanol was added after 4 hours incubation at -20 °C. cDNA, synthesized from extracted RNA, was amplified and purified using the WT-Ovation™ Pico RNA Amplification System (NuGEN, San Carlos, CA) and the DNA Clean & Concentrator™-25 (Zymo Research, Orange, CA). RNA library preparation protocol: biotin Samples were labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN, San Carlos, CA).

Reference

PMID: 19474297 Title: Functional genomic analysis of amniotic fluid cell-free mRNA suggests that oxidative stress is significant in Down syndrome fetuses Author: Slonim DK, Koide K, Johnson KL, Tantravahi U, Cowan JM, Jarrah Z, Bianchi DW Journal: Proc Natl Acad Sci U S A. 2009 Jun 9;106(23):9425-9. Description: To characterize the differences between second trimester Down syndrome (DS) and euploid fetuses, we used Affymetrix microarrays to compare gene expression in uncultured amniotic fluid supernatant samples.