exRNAdisease

Entry Detail

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General Information

Database ID: exR0000124 RNA Name: ACAT1 RNA Type: mRNA Chromosome: chr11 Starnd: + Coordinate: Start Site(bp): 108116695 End Site(bp): 108147603 External Links: ENSG00000075239

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 ATP2A2 chr12 110280756 110351093 + MTRNR2L8 chr11 10507894 10509186 - TRIP10 chr19 6737925 6751530 + NPEPPS chr17 47522942 47623276 + DAPK1 chr9 87497228 87708634 + PSMB5 chr14 23016543 23035230 - CCDC102A chr16 57512181 57536571 - FZD3 chr8 28494205 28574267 + NCAM1 chr11 112961247 113278436 + PRDX4 chrX 23664262 23686397 + PSMD10 chrX 108084207 108091549 - PGK1 chrX 77910739 78129295 + HSP90AB1 chr6 44246166 44253888 + NPIPB2 chr16 11927259 11976643 - TXNRD1 chr12 104215779 104350307 + MRPL47 chr3 179588285 179604649 - AC010422.3 chr19 12643831 12648397 - GHITM chr10 84139509 84153568 + POU3F3 chr2 104853287 104858574 + RPS4X chrX 72255679 72277248 - DAP3 chr1 155687960 155739010 + EEF1A1 chr6 73515750 73523797 - GLI2 chr2 120735623 120992653 + IER3IP1 chr18 47152834 47176364 - RPLP1 chr15 69452814 69456205 + ACTG1 chr17 81509971 81523847 - IGFBP2 chr2 216632828 216664436 + NUP205 chr7 135557917 135648757 + ACTB chr7 5527148 5563784 - TXNDC16 chr14 52430596 52552522 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand MIR155HG chr21 25561909 25575168 + POLR2J4 chr7 43940895 44019175 - 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.