exRNAdisease

Entry Detail

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General Information

Database ID: exR0000371 RNA Name: AGFG2 RNA Type: mRNA Chromosome: chr7 Starnd: + Coordinate: Start Site(bp): 100539203 End Site(bp): 100568220 External Links: ENSG00000106351

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 HK1 chr10 69269984 69401884 + DUSP2 chr2 96143169 96145440 - HMGA1 chr6 34236873 34246231 + ADCY3 chr2 24819169 24919839 - BLCAP chr20 37492472 37527931 - KCNQ5 chr6 72621792 73198851 + LASP1 chr17 38869859 38921770 + RPS5 chr19 58386400 58394806 + CORO1B chr11 67435510 67443821 - RBM42 chr19 35629030 35637686 + DDX5 chr17 64498254 64508199 - RPS19 chr19 41860255 41872925 + REEP5 chr5 112876385 112922289 - HLA-A chr6 29941260 29945884 + VPS4A chr16 69311350 69326939 + SLC12A8 chr3 125082636 125212864 - ZFP36L1 chr14 68787660 68796253 - HLA-E chr6 30489509 30494194 + ARID3A chr19 925781 975939 + RPL13 chr16 89560657 89566828 + PTPRCAP chr11 67435510 67437682 - SOX13 chr1 204073115 204127743 + NMT1 chr17 45051610 45109016 + CRKL chr22 20917407 20953747 + INAFM2 chr15 40323692 40326715 + CDK1 chr10 60778331 60794852 + TUBA1B chr12 49127782 49131397 - BASP1 chr5 17065598 17276843 + TMEM54 chr1 32894594 32901438 - TPT1 chr13 45333471 45341370 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC009065.3 chr16 2091436 2095433 + TMEM147-AS1 chr19 35540738 35546029 - 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.