exRNAdisease

Entry Detail

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General Information

Database ID: exR0000338 RNA Name: ADRM1 RNA Type: mRNA Chromosome: chr20 Starnd: + Coordinate: Start Site(bp): 62302093 End Site(bp): 62308862 External Links: ENSG00000130706

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 DDIT4 chr10 72273924 72276036 + MIER2 chr19 301444 344815 - TOPBP1 chr3 133598175 133662380 - HLA-B chr6 31269491 31357188 - NPLOC4 chr17 81556887 81648465 - P2RY11 chr19 10111693 10115372 + TAGLN2 chr1 159918107 159925732 - SREBF2 chr22 41833079 41907307 + TUBA1B chr12 49127782 49131397 - DDX49 chr19 18919705 18929189 + SELENOH chr11 57741250 57743554 + U2AF2 chr19 55654146 55674715 + RPS9 chr19 54200809 54249003 + MT-ND3 chrMT 10059 10404 + PLEC chr8 143915147 143976734 - TEX261 chr2 70985942 70994873 - OTUB1 chr11 63985853 64001811 + GNAO1 chr16 56191489 56357444 + GABARAP chr17 7240008 7242449 - VPS28 chr8 144423601 144428563 - ENO1 chr1 8861000 8879190 - TMEM8B chr9 35814451 35865518 + HSP90AB1 chr6 44246166 44253888 + TMEM120B chr12 121712752 121783001 + NDUFV1 chr11 67605653 67612554 + EMG1 chr12 6970913 6997428 + MTREX chr5 55307989 55425579 + MT-CO3 chrMT 9207 9990 + RGMB chr5 98768650 98798643 + ACAP3 chr1 1292390 1309609 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC139530.1 chr17 81701324 81703300 - BX284668.2 chr1 16870945 16883659 + 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.