exRNAdisease

General Information

Database ID:

exR0000116

RNA Name:

ACADM

RNA Type:

mRNA

Chromosome:

chr1

Starnd:

Coordinate:

Start Site(bp):

75724347

End Site(bp):

75787575

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
DBN1	chr5	177456608	177474401	-
HMGA1	chr6	34236873	34246231	+
ARID5A	chr2	96536743	96552634	+
RPN2	chr20	37178410	37241619	+
HACD3	chr15	65530418	65578349	+
ITGB3BP	chr1	63440770	63593721	-
HYOU1	chr11	119044188	119057227	-
SLC35G1	chr10	93893973	93956062	+
RBMXL1	chr1	88979456	88992960	-
DTX4	chr11	59171430	59208588	+
FOXN2	chr2	48314637	48379295	+
PNN	chr14	39175183	39183220	+
BUB1B	chr15	40161023	40221136	+
DDX39B	chr6	31530219	31542448	-
GDI2	chr10	5765223	5842132	-
FTL	chr19	48965309	48966879	+
PKM	chr15	72199029	72231822	-
SRRM1	chr1	24631716	24673281	+
EXOSC8	chr13	36998816	37009614	+
DHX8	chr17	43483865	43610338	+
TRPC4	chr13	37636636	37870425	-
POLDIP3	chr22	42583721	42614962	-
RPL30	chr8	98024851	98046469	-
COA7	chr1	52684449	52698347	-
DNMT3B	chr20	32762385	32809356	+
ATP6V1G2-DDX39B	chr6	31530219	31546608	-
RPS24	chr10	78033760	78056813	+
NR1H2	chr19	50329653	50383388	+
NCOA4	chr10	46005088	46030714	-
XPO1	chr2	61477849	61538626	-

miRNA targets:

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC004812.2	chr12	120116907	120119000	+
AC009948.2	chr2	178548884	178550681	+
AC069287.1	chr11	112967	125927	-
AL831711.1	chr1	161433444	161440996	-

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.