exRNAdisease

Entry Detail

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General Information

Database ID: exR0000343 RNA Name: AEN RNA Type: mRNA Chromosome: chr15 Starnd: + Coordinate: Start Site(bp): 88621337 End Site(bp): 88632281 External Links: ENSG00000181026

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 HSP90AA1 chr14 102080738 102139699 - PTEN chr10 87863625 87971930 + MAPK9 chr5 180233143 180292099 - PABPC1 chr8 100685816 100722809 - ITM2C chr2 230864639 230879248 + KAT7 chr17 49788681 49835026 + HCCS chrX 11111301 11123086 + MESD chr15 80946289 80989828 - PPP1CB chr2 28751640 28802940 + PEBP1 chr12 118136124 118145584 + STARD7 chr2 96184859 96208825 - YBX1 chr1 42682418 42703805 + MYL6 chr12 56158161 56163496 + STRN4 chr19 46719511 46746994 - AC006538.2 chr19 2717769 2740048 - APH1A chr1 150265399 150269580 - JUNB chr19 12791486 12793315 + TSR2 chrX 54440404 54448032 + PLK1 chr16 23677656 23690367 + MATK chr19 3777970 3802129 - CSDE1 chr1 114716913 114758676 - FKBP8 chr19 18531751 18544077 - TOR1A chr9 129812942 129824244 - R3HDM2 chr12 57253762 57431005 - GBE1 chr3 81489703 81761645 - IVD chr15 40405485 40435947 + GPBP1 chr5 57173948 57264679 + ZNF202 chr11 123723914 123741675 - HSPA4 chr5 133052013 133106449 + MDK chr11 46380756 46383837 + miRNA targets: miRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand hsa-miR-24-3p chr9 95086064 95086085 + hsa-miR-27a-3p chr19 13836447 13836467 - hsa-miR-101-3p chr1 65058442 65058462 - hsa-miR-27b-3p chr9 95085505 95085525 + hsa-miR-513a-5p chrX 147213538 147213555 - hsa-miR-455-5p chr9 114209449 114209470 + circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC007952.4 chr17 19112000 19112636 - AC093827.4 chr4 86924630 86936202 - AD000090.1 chr19 35557956 35581954 + CCDC183-AS1 chr9 136803927 136808848 - LNCPRESS1 chr7 101299578 101301346 + NEAT1 chr11 65422774 65445540 + SNHG3 chr1 28505980 28510892 + XIST chrX 73820649 73852723 - ZFAS1 chr20 49278178 49299600 + 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.