exRNAdisease

General Information

Database ID:

exR0000274

RNA Name:

ADAR

RNA Type:

mRNA

Chromosome:

chr1

Starnd:

Coordinate:

Start Site(bp):

154582057

End Site(bp):

154628013

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
KIAA0040	chr1	175156986	175192999	-
HLA-B	chr6	31269491	31357188	-
AC007192.1	chr19	18153158	18178117	+
TMSB4X	chrX	12975110	12977227	+
NTAN1	chr16	15037854	15056079	-
RPS14	chr5	150442635	150449739	-
CLCN6	chr1	11806096	11848079	+
KAT7	chr17	49788681	49835026	+
SIK3	chr11	116843402	117098437	-
TMEM147	chr19	35545600	35547526	+
MAN2C1	chr15	75355207	75368612	-
LPXN	chr11	58526871	58578220	-
AURKB	chr17	8204733	8210600	-
SSR1	chr6	7268306	7347446	-
DHCR24	chr1	54849627	54887195	-
RPS8	chr1	44775251	44778779	+
ATP5PF	chr21	25716503	25735673	-
RPL27A	chr11	8682788	8714759	+
TMEM69	chr1	45688181	45694436	+
TMED10	chr14	75131469	75176612	-
PACSIN2	chr22	42835412	43015149	-
UFM1	chr13	38349849	38363619	+
OAS3	chr12	112938444	112973251	+
SRC	chr20	37344685	37406050	+
ERP29	chr12	112013348	112023449	+
HLA-DPA1	chr6	33064569	33080775	-
ZFR	chr5	32354350	32444740	-
CAPRIN1	chr11	34051731	34102610	+
PKM	chr15	72199029	72231822	-
STARD7	chr2	96184859	96208825	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-130b-3p	chr22	21653354	21653375	+
hsa-miR-373-3p	chr19	53788748	53788770	+
hsa-miR-520e-3p	chr19	53675764	53675784	+
hsa-miR-519c-3p	chr19	53686522	53686543	+
hsa-miR-519b-3p	chr19	53695263	53695284	+
hsa-miR-520b-3p	chr19	53701267	53701287	+
hsa-miR-520c-3p	chr19	53707506	53707527	+
hsa-miR-4426	chr1	192716333	192716349	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC009163.4	chr16	75458252	75460017	-
AC135178.2	chr17	8318088	8318712	-
AL139819.1	chr10	100335563	100346390	-
LHFPL3-AS2	chr7	104894628	104926645	-
LINC01273	chr20	50171809	50176676	+
RMST	chr12	97430884	97598415	+
THAP7-AS1	chr22	21001886	21010342	+
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.