exRNAdisease

General Information

Database ID:

exR0000108

RNA Name:

ACAA2

RNA Type:

mRNA

Chromosome:

chr18

Starnd:

Coordinate:

Start Site(bp):

49782164

End Site(bp):

49813953

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
DCAF5	chr14	69050881	69153150	-
PSMA6	chr14	35278633	35317493	+
RPL13	chr16	89560657	89566828	+
GSPT1	chr16	11868128	11916082	-
GABARAP	chr17	7240008	7242449	-
DNAJC1	chr10	21756548	22003769	-
LRRN1	chr3	3799431	3849834	+
SRSF7	chr2	38743599	38751494	-
MAPKAP1	chr9	125437393	125707234	-
CLDND1	chr3	98497912	98523066	-
AC120057.2	chr17	7240427	7244635	-
KDM5C	chrX	53191321	53225422	-
RAB6A	chr11	73675638	73761137	-
EXOC6B	chr2	72175984	72826041	-
CDC20	chr1	43358981	43363203	+
SF3B6	chr2	24067586	24076373	-
UBL5	chr19	9827892	9830115	+
MTRNR2L12	chr3	96617188	96618236	-
HACD4	chr9	20999509	21031640	-
RAN	chr12	130872037	130877678	+
RAD17	chr5	69369293	69414801	+
RPS6	chr9	19375715	19380236	-
REEP5	chr5	112876385	112922289	-
LRRFIP1	chr2	237627587	237813682	+
VASP	chr19	45506579	45526983	+
CAPN1	chr11	65180566	65212006	+
CKAP5	chr11	46743048	46846308	-
NTS	chr12	85874295	85882992	+
ERN1	chr17	64039142	64130819	-
PRDX6	chr1	173477330	173488815	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-492	chr12	94834427	94834449	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC026362.1	chr12	122975320	122982907	+
AD000090.1	chr19	35557956	35581954	+

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.