exRNAdisease

General Information

Database ID:

exR0000052

RNA Name:

ABCC4

RNA Type:

mRNA

Chromosome:

chr13

Starnd:

Coordinate:

Start Site(bp):

95019835

End Site(bp):

95301475

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
KIF7	chr15	89608789	89655467	-
ERFE	chr2	238158970	238168900	+
POLR3D	chr8	22245133	22254601	+
SLC5A6	chr2	27199587	27212958	-
PIGC	chr1	172370189	172444086	-
AC007192.1	chr19	18153158	18178117	+
NDUFA10	chr2	239892450	240025345	-
ZBTB21	chr21	41986831	42010387	-
RUVBL1	chr3	128064778	128153914	-
ZDHHC20	chr13	21372573	21459370	-
IFI6	chr1	27666064	27672198	-
MYO1G	chr7	44962662	44979088	-
DPPA4	chr3	109326141	109337572	-
CCT8	chr21	29055805	29073797	-
BASP1	chr5	17065598	17276843	+
FNBP1	chr9	129887187	130043194	-
LTBP4	chr19	40592883	40629818	+
LARP1	chr5	154712843	154817605	+
RPL4	chr15	66498015	66524532	-
RRM1	chr11	4094707	4138932	+
SPOUT1	chr9	128819651	128829794	-
LLGL2	chr17	75525080	75575208	+
SACS	chr13	23328826	23433740	-
RPL27A	chr11	8682788	8714759	+
YIPF5	chr5	144158162	144170714	-
SRP14	chr15	40035690	40039181	-
FKBP8	chr19	18531751	18544077	-
KMT2B	chr19	35717973	35738878	+
DDX41	chr5	177511577	177516961	-
ING3	chr7	120950763	120977216	+

miRNA targets:

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
CRTC3-AS1	chr15	90620007	90717141	-
DLEU1	chr13	50082169	50906856	+
MALAT1	chr11	65497688	65506516	+
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.