exRNAdisease

General Information

Database ID:

exR0000359

RNA Name:

AGAP3

RNA Type:

mRNA

Chromosome:

chr7

Starnd:

Coordinate:

Start Site(bp):

151085831

End Site(bp):

151144436

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
ZNF703	chr8	37695782	37700019	+
INTS1	chr7	1470277	1504389	-
AC010646.1	chr19	17235940	17255448	-
RNF11	chr1	51236273	51273447	+
SLC31A1	chr9	113221544	113264492	+
GFM1	chr3	158644278	158692575	+
NR2F6	chr19	17231883	17245940	-
DOCK1	chr10	126905409	127452517	+
TMEM181	chr6	158536436	158635428	+
TMEM241	chr18	23197144	23437961	-
CDC25A	chr3	48157146	48188417	-
POU5F1B	chr8	127322183	127420066	+
LONP1	chr19	5691834	5720572	-
KRT10	chr17	40818117	40822614	-
XYLT2	chr17	50346126	50363138	+
KDM4B	chr19	4969113	5153598	+
BSG	chr19	571277	583493	+
RPS6	chr9	19375715	19380236	-
PDGFA	chr7	497258	520296	-
FAM219B	chr15	74899992	74906883	-
HOXD11	chr2	176104216	176109754	+
ADA	chr20	44619522	44652233	-
HMGA1	chr6	34236873	34246231	+
CDK18	chr1	205504595	205532793	+
SLC25A39	chr17	44319625	44324870	-
ADIPOR1	chr1	202940826	202958572	-
MT-ND4L	chrMT	10470	10766	+
INA	chr10	103277138	103290346	+
WDR6	chr3	49007062	49015953	+
BUB3	chr10	123154402	123170467	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-299-5p	chr14	101023800	101023821	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC022400.3	chr10	73674295	73730466	-
AC087741.1	chr17	80200673	80205949	-
AC079949.1	chr12	127142029	127146532	-
AL355472.2	chr1	234357006	234365828	+
AL356488.2	chr1	109100193	109100619	+
FGD5-AS1	chr3	14920347	14948424	-
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.