exRNAdisease

Entry Detail

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General Information

Database ID: exR0000007 RNA Name: AAAS RNA Type: mRNA Chromosome: chr12 Starnd: - Coordinate: Start Site(bp): 53307456 End Site(bp): 53324864 External Links: ENSG00000094914

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 MSI1 chr12 120341330 120369164 - RPL11 chr1 23691742 23696835 + RPLP2 chr11 809965 812880 + MIF chr22 23894383 23895227 + MRPS10 chr6 42206807 42217861 - RCSD1 chr1 167630093 167708696 + LRCH4 chr7 100574011 100586129 - LRP2 chr2 169127109 169362534 - MEX3C chr18 51174550 51218304 - MTRNR2L12 chr3 96617188 96618236 - MTA1 chr14 105419820 105470729 + B2M chr15 44711487 44718877 + CDC25B chr20 3786772 3806121 + SFPQ chr1 35176378 35193145 - ZNF207 chr17 32350117 32381886 + VPS41 chr7 38722974 38932394 - RPL13 chr16 89560657 89566828 + METTL16 chr17 2405562 2511891 - MAPK14 chr6 36027677 36111236 + CD99 chrX 2691187 2741309 + YBX3 chr12 10699089 10723323 - AP000350.4 chr22 23862188 23895223 + PKM chr15 72199029 72231822 - FRAS1 chr4 78057323 78544269 + LRIG1 chr3 66378797 66501263 - RACK1 chr5 181236897 181248096 - ALDOA chr16 30064164 30070457 + MYL6 chr12 56158161 56163496 + NBR1 chr17 43170481 43211689 + LAMA5 chr20 62307955 62367312 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC069281.2 chr7 100572232 100578700 - PCAT6 chr1 202810954 202812156 + XIST chrX 73820649 73852723 - 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.