exRNAdisease

General Information

Database ID:

exR0000357

RNA Name:

AGAP1

RNA Type:

mRNA

Chromosome:

chr2

Starnd:

Coordinate:

Start Site(bp):

235494043

End Site(bp):

236131800

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
KAT2A	chr17	42113111	42121367	-
LIN54	chr4	82909973	83012926	-
ENAH	chr1	225486835	225653142	-
OXSR1	chr3	38165089	38255484	+
NCOR2	chr12	124324415	124567589	-
LMAN2	chr5	177331567	177351668	-
NFATC2IP	chr16	28950807	28967097	+
C14orf132	chr14	96039324	96093889	+
HES6	chr2	238238267	238240662	-
SELENOW	chr19	47778585	47784686	+
HDAC3	chr5	141620876	141636849	-
CUL3	chr2	224470150	224585397	-
RPUSD1	chr16	784974	788397	-
SNX10	chr7	26291895	26374329	+
CNOT1	chr16	58519951	58629885	-
MEIS1	chr2	66433452	66573869	+
GIGYF2	chr2	232697299	232860575	+
TEX264	chr3	51662693	51704323	+
KIF1A	chr2	240713761	240821036	-
RPS27A	chr2	55231903	55235853	+
GNAS	chr20	58839718	58911192	+
TRAIP	chr3	49828601	49856574	-
GDAP2	chr1	117863485	117929621	-
DYNC1LI1	chr3	32525974	32570858	-
SLX1A	chr16	30193887	30197561	+
LRBA	chr4	150264435	151015727	-
GAPDH	chr12	6534512	6538374	+
PSMD7	chr16	74296814	74306288	+
SIPA1L2	chr1	232397965	232561558	-
HMGA2	chr12	65824131	65966295	+

miRNA targets:

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC022400.3	chr10	73674295	73730466	-
AGAP1-IT1	chr2	235505751	235507566	+
AGAP11	chr10	86970741	87010126	+
AL136982.1	chr10	86992406	87010203	+
NOP14-AS1	chr4	2934882	2961738	+
SLX1A-SULT1A3	chr16	30193892	30204310	+
TMEM147-AS1	chr19	35540738	35546029	-
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.