exRNAdisease

Entry Detail

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General Information

Database ID: exR0000223 RNA Name: ADA RNA Type: mRNA Chromosome: chr20 Starnd: - Coordinate: Start Site(bp): 44619522 End Site(bp): 44652233 External Links: ENSG00000196839

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 S100A11 chr1 152032506 152047907 - ELOVL5 chr6 53267398 53349179 - SSR4 chrX 153793516 153798499 + HSP90AB1 chr6 44246166 44253888 + WASHC3 chr12 102012840 102062149 - RAB14 chr9 121178133 121223014 - LAT2 chr7 74199652 74229834 + EEF1A1 chr6 73515750 73523797 - CDKN1A chr6 36676460 36687339 + ZNF703 chr8 37695782 37700019 + NACA chr12 56712427 56731628 - SEC62 chr3 169966635 169998373 + HLA-C chr6 31268749 31272130 - SRSF4 chr1 29147743 29181900 - URB1 chr21 32311018 32393012 - GYPC chr2 126656133 126696667 + PEX5 chr12 7188685 7218574 + AGAP3 chr7 151085831 151144436 + XRCC5 chr2 216107464 216206303 + DVL2 chr17 7225342 7234517 - RPS19 chr19 41860255 41872925 + EVL chr14 99971449 100144236 + MRPL38 chr17 75898643 75905413 - RPL27A chr11 8682788 8714759 + RALY chr20 33993646 34108308 + TUBA1B chr12 49127782 49131397 - NPC2 chr14 74476192 74494177 - CD81 chr11 2376177 2397419 + DRAP1 chr11 65919274 65921563 + SORD chr15 45023181 45077185 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AL359924.1 chr1 237862175 237928321 + LINC00996 chr7 150433654 150448140 + SNHG1 chr11 62851984 62855953 - 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.