exRNAdisease

General Information

Database ID:

exR0000029

RNA Name:

ABCA2

RNA Type:

mRNA

Chromosome:

chr9

Starnd:

Coordinate:

Start Site(bp):

137007234

End Site(bp):

137028922

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
STK11	chr19	1177558	1228431	+
SLC36A4	chr11	93144174	93197991	-
KBTBD11	chr8	1973677	2006936	+
BMP2K	chr4	78776342	78916372	+
EXOC7	chr17	76081016	76121576	-
SMG5	chr1	156249224	156282825	-
SPECC1L	chr22	24270817	24417739	+
XXYLT1	chr3	195068284	195271159	-
NIP7	chr16	69337996	69343106	+
MYL5	chr4	673580	682033	+
RBPJ	chr4	26163455	26435131	+
REEP5	chr5	112876385	112922289	-
GANAB	chr11	62624826	62646726	-
DDX6	chr11	118747763	118791164	-
METTL26	chr16	634427	636366	-
ACAP3	chr1	1292390	1309609	-
LRP5	chr11	68312591	68449275	+
SUPT5H	chr19	39436156	39476670	+
MCM2	chr3	127598410	127622436	+
HNRNPK	chr9	83968083	83980616	-
FLNA	chrX	154348524	154374638	-
SRRM2	chr16	2752626	2772538	+
POMGNT1	chr1	46188682	46220305	-
PLXNA1	chr3	126988594	127037392	+
HDGFL3	chr15	83112738	83207823	-
YWHAQ	chr2	9583967	9630997	-
LMAN2	chr5	177331567	177351668	-
HECA	chr6	139135080	139180802	+
SEC24C	chr10	73744372	73772161	+
EXTL3	chr8	28600469	28755599	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-1286	chr22	20249145	20249165	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC016876.2	chr17	7581964	7584086	-
AC067930.1	chr8	143579636	143580670	+
AD000090.1	chr19	35557956	35581954	+
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.