exRNAdisease

General Information

Database ID:

exR0000378

RNA Name:

AGO3

RNA Type:

mRNA

Chromosome:

chr1

Starnd:

Coordinate:

Start Site(bp):

35930718

End Site(bp):

36072500

External Links:

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
DVL3	chr3	184155377	184173614	+
FBXL19	chr16	30923055	30948783	+
ATAD3B	chr1	1471765	1497848	+
PPP1R12C	chr19	55090914	55117637	-
TXNIP	chr1	145992435	145996579	-
WASF2	chr1	27404230	27490167	-
ADORA2B	chr17	15944917	15975746	+
MGLL	chr3	127689062	128052190	-
PDIA5	chr3	123067025	123225227	+
SSR3	chr3	156540140	156555184	-
MYCBP2	chr13	77044657	77327094	-
SNRPN	chr15	24823637	24978723	+
DVL1	chr1	1335276	1349418	-
RPL13	chr16	89560657	89566828	+
ZNF775	chr7	150368790	150398630	+
SLC5A6	chr2	27199587	27212958	-
CAPN15	chr16	527712	554636	+
PAICS	chr4	56435741	56464579	+
ALKBH6	chr19	36009120	36014239	-
CHD3	chr17	7884796	7912760	+
FAM126B	chr2	200973718	201071671	-
RIMBP3B	chr22	21383374	21389478	+
AC073111.4	chr7	150400702	150412470	+
SPAG5	chr17	28577565	28599025	-
YBX1	chr1	42682418	42703805	+
PPA2	chr4	105369077	105474067	-
MT-ND4L	chrMT	10470	10766	+
VPS13B	chr8	99013266	99877580	+
RPS3	chr11	75399515	75422280	+
DIP2A	chr21	46458891	46570015	+

miRNA targets:

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC002116.1	chr19	36008638	36014235	-
AC007952.4	chr17	19112000	19112636	-
AC108136.1	chr8	122485515	122489815	-
AC079949.1	chr12	127142029	127146532	-
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.