exRNAdisease

General Information

Database ID:

exR0000292

RNA Name:

ADCY9

RNA Type:

mRNA

Chromosome:

chr16

Starnd:

Coordinate:

Start Site(bp):

3953387

End Site(bp):

4116442

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
CHMP1A	chr16	89644435	89657721	-
MAN2A1	chr5	109689366	109869625	+
CHMP2A	chr19	58551566	58555105	-
CXXC1	chr18	50282343	50288304	-
C11orf24	chr11	68261338	68272001	-
RC3H2	chr9	122844556	122905359	-
LRFN3	chr19	35935358	35946624	+
PPIB	chr15	64155812	64163205	-
BRWD1	chr21	39184176	39321559	-
RRP7A	chr22	42508344	42519796	-
SPTAN1	chr9	128552558	128633662	+
SF3A2	chr19	2236824	2248655	+
TBCB	chr19	36114289	36125947	+
INTS11	chr1	1311585	1324691	-
PLCG2	chr16	81739097	81962685	+
DDX39B	chr6	31530219	31542448	-
HUWE1	chrX	53532096	53686728	-
TAF5L	chr1	229593111	229626047	-
DPM2	chr9	127935099	127938484	-
POLG	chr15	89305198	89334861	-
UBE2M	chr19	58555712	58558954	-
JMJD8	chr16	681670	684528	-
LGR5	chr12	71439798	71586310	+
AKT1	chr14	104769349	104795751	-
MAN2C1	chr15	75355207	75368612	-
HMBOX1	chr8	28890395	29064764	+
PTPRF	chr1	43525187	43623666	+
PROB1	chr5	139390592	139395104	-
MON1B	chr16	77190835	77202398	+
AMIGO3	chr3	49716829	49719684	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-25-3p	chr7	100093571	100093592	-
hsa-miR-33a-5p	chr22	41900949	41900969	+
hsa-miR-147a	chr9	120244985	120245004	-
hsa-miR-218-5p	chr5	168768211	168768231	-
hsa-miR-367-3p	chr4	112647877	112647898	-
hsa-miR-338-3p	chr17	81125887	81125908	-
hsa-miR-92b-3p	chr1	155195237	155195258	+
hsa-miR-33b-5p	chr17	17813897	17813916	-
hsa-miR-541-3p	chr14	101064548	101064569	+
hsa-miR-147b-3p	chr15	45433098	45433118	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
LINC00265	chr7	39733430	39793092	+

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.