exRNAdisease

General Information

Database ID:

exR0009528

RNA Name:

NME2

RNA Type:

mRNA

Chromosome:

chr17

Starnd:

Coordinate:

Start Site(bp):

51165435

End Site(bp):

51171747

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
AAR2	chr20	36236459	36270918	+
AASDHPPT	chr11	106075501	106098699	+
ABHD6	chr3	58237532	58295693	+
AC004832.3	chr22	30409255	30428990	+
AC005258.1	chr19	2269525	2341172	+
AC006030.1	chr2	74211604	74363377	-
AC010422.3	chr19	12643831	12648397	-
AC104472.3	chr3	155763043	155854442	-
AC120057.2	chr17	7240427	7244635	-
AC131160.1	chr3	183815568	183884889	-
AC139530.2	chr17	81703371	81720539	+
ACACA	chr17	37084992	37406836	-
ACBD6	chr1	180269653	180502954	-
ACIN1	chr14	23058564	23095614	-
ACTB	chr7	5527148	5563784	-
ACTG1	chr17	81509971	81523847	-
ACVR2B	chr3	38453890	38493142	+
ADAR	chr1	154582057	154628013	-
ADAT1	chr16	75596981	75623300	-
ADGRG6	chr6	142301854	142446266	+
AKAP1	chr17	57085092	57121346	+
AKAP8L	chr19	15380050	15419141	-
AKAP9	chr7	91940867	92110673	+
AKIRIN1	chr1	38991276	39006059	+
AKR1A1	chr1	45550543	45570049	+
AL133352.1	chr10	100505628	100529881	-
AL513165.2	chr9	37512547	37592469	-
AL590764.2	chrX	71103987	71111575	-
ALDH2	chr12	111766887	111817532	+
ALDOA	chr16	30064164	30070457	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-206	chr6	52144401	52144422	+
hsa-miR-302c-3p	chr4	112648366	112648388	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC004224.2	chr16	3458071	3515564	+
AC020915.3	chr19	58257270	58278808	-
AC132217.1	chr11	2129121	2129964	-
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.