exRNAdisease

Entry Detail

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General Information

Database ID: exR0006377 RNA Name: HLA-DQA1 RNA Type: mRNA Chromosome: chr6 Starnd: + Coordinate: Start Site(bp): 32628179 End Site(bp): 32647062 External Links: ENSG00000196735

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 ABCF1 chr6 30571393 30597179 + ABI2 chr2 203328239 203447728 + AC006538.2 chr19 2717769 2740048 - AC007192.1 chr19 18153158 18178117 + AC007998.2 chr18 35443871 35497940 - AC011448.1 chr19 19516227 19536076 + AC011462.1 chr19 41350853 41425001 + AC026464.4 chr16 69299682 69322700 + AC068580.4 chr11 1734821 1763954 - AC073082.1 chr2 48632291 48755724 - ACAD11 chr3 132558138 132660082 - ACAD8 chr11 134253495 134265855 + ACTA2 chr10 88935074 88991339 - ACTB chr7 5527148 5563784 - ACTG1 chr17 81509971 81523847 - ACTR3 chr2 113890063 113962596 + ADPRHL2 chr1 36088892 36093932 + AHCY chr20 34280268 34311802 - AHRR chr5 271670 438291 + AIFM1 chrX 130129362 130165887 - AL021997.3 chr6 28267121 28281580 + AL136454.1 chr1 192716132 192716653 + ALDOA chr16 30064164 30070457 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC005083.1 chr7 20217577 20221700 + AC005899.4 chr17 32328441 32329395 + AC007996.1 chr18 26542971 26545791 - AC010618.3 chr19 17488990 17511889 - AC012236.1 chr15 31221999 31230838 - AC019205.1 chr6 73263212 73301789 + AC099329.1 chr3 42785087 42852428 - AC107027.3 chr3 131455126 131458598 - AD000090.1 chr19 35557956 35581954 + AL031428.1 chr1 23020147 23088058 - 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.