exRNAdisease

General Information

Database ID:

exR0000494

RNA Name:

ALDH9A1

RNA Type:

mRNA

Chromosome:

chr1

Starnd:

Coordinate:

Start Site(bp):

165662216

End Site(bp):

165698863

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
FYN	chr6	111660332	111873452	-
NIPSNAP1	chr22	29554808	29581327	-
GSE1	chr16	85169525	85676204	+
KCNMB4	chr12	70366290	70434292	+
RPS15	chr19	1438358	1440494	+
HES1	chr3	194136148	194138732	+
B4GALT6	chr18	31622247	31685836	-
FBRSL1	chr12	132489551	132585188	+
TCF19	chr6	31158547	31167159	+
RABEP2	chr16	28904421	28936526	-
MORF4L2	chrX	103675496	103688158	-
PCK2	chr14	24094053	24110598	+
LRRFIP1	chr2	237627587	237813682	+
SRSF2	chr17	76734115	76737374	-
ITCH	chr20	34363241	34540748	+
ZNF384	chr12	6666477	6689572	-
SPARC	chr5	151661096	151686975	-
CD55	chr1	207321376	207386804	+
ENO1	chr1	8861000	8879190	-
RPS6	chr9	19375715	19380236	-
DDOST	chr1	20651767	20661544	-
SRSF3	chr6	36594353	36605600	+
KHSRP	chr19	6413348	6424794	-
RALY	chr20	33993646	34108308	+
SLC4A8	chr12	51391317	51515763	+
MRRF	chr9	122264603	122331337	+
MCM7	chr7	100092728	100101940	-
DVL3	chr3	184155377	184173614	+
GJA1	chr6	121435595	121449727	+
MTA1	chr14	105419820	105470729	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-92a-3p	chrX	134169544	134169565	-
hsa-miR-1270	chr19	20399320	20399342	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC026740.1	chr5	675826	676616	+
AL139819.1	chr10	100335563	100346390	-

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.