exRNAdisease

General Information

Database ID:

exR0000060

RNA Name:

ABCD4

RNA Type:

mRNA

Chromosome:

chr14

Starnd:

Coordinate:

Start Site(bp):

74285269

End Site(bp):

74303055

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
QSER1	chr11	32892820	32993316	+
MRPL46	chr15	88459477	88467390	-
MXRA8	chr1	1352689	1361777	-
NSUN2	chr5	6599239	6633291	-
M6PR	chr12	8940361	8949761	-
SIK1	chr21	43414483	43427131	-
RPL10	chrX	154389955	154409168	+
SFI1	chr22	31488688	31618588	+
C5orf24	chr5	134845680	134859735	+
RDH13	chr19	55039108	55071291	-
CRYL1	chr13	20403666	20525873	-
LONRF3	chrX	118974614	119018355	+
ORC3	chr6	87590067	87667453	+
ACOT8	chr20	45841721	45857405	-
TP53RK	chr20	46684365	46689444	-
ZNF668	chr16	31060843	31074240	-
PFN1	chr17	4945652	4949061	-
LTK	chr15	41503637	41513887	-
TOMM40L	chr1	161225939	161230746	+
FBXW4	chr10	101610664	101695295	-
NEO1	chr15	73051710	73305205	+
SELENOS	chr15	101270817	101277500	-
NHP2	chr5	178149460	178153967	-
EIF4H	chr7	74174245	74197101	+
HSP90AB1	chr6	44246166	44253888	+
BTBD2	chr19	1985438	2034881	-
TRIP13	chr5	892884	919357	+
HSPA4	chr5	133052013	133106449	+
CCDC167	chr6	37482938	37499893	-
VMP1	chr17	59707192	59842255	+

miRNA targets:

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC005519.1	chr14	74289127	74294425	-
AC005562.1	chr17	30576464	30672789	+
AC007952.4	chr17	19112000	19112636	-
AC011476.2	chr19	55027593	55053928	-
MALAT1	chr11	65497688	65506516	+

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.