exRNAdisease

General Information

Database ID:

exR0000209

RNA Name:

ACTR6

RNA Type:

mRNA

Chromosome:

chr12

Starnd:

Coordinate:

Start Site(bp):

100199122

End Site(bp):

100241865

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
ANKFY1	chr17	4163821	4263995	-
DDX24	chr14	94048287	94081212	-
AP002990.1	chr11	62559603	62591531	-
CD52	chr1	26317958	26320523	+
HNRNPC	chr14	21209136	21269494	-
RPS23	chr5	82273320	82278396	-
NAGK	chr2	71064344	71079808	+
EEF1G	chr11	62559596	62574086	-
RPL13	chr16	89560657	89566828	+
IGF2	chr11	2129112	2141238	-
UBE2D3	chr4	102794383	102868896	-
CD81	chr11	2376177	2397419	+
VSIG10	chr12	118063593	118136026	-
TMEM123	chr11	102396332	102470384	-
ACTB	chr7	5527148	5563784	-
GYG2	chrX	2828822	2882820	+
RAB35	chr12	120095099	120117502	-
NSUN5	chr7	73302516	73308826	-
HLA-C	chr6	31268749	31272130	-
ATP6AP2	chrX	40579372	40606848	+
FTH1	chr11	61959718	61967634	-
MTRNR2L12	chr3	96617188	96618236	-
ADH5	chr4	99070978	99088801	-
CLEC2D	chr12	9664969	9699553	+
NONO	chrX	71283192	71301168	+
RPS7	chr2	3575260	3580920	+
ZNF90	chr19	20077994	20127076	+
SLAMF1	chr1	160608106	160647295	-
ST8SIA1	chr12	22063773	22437041	-
YIPF3	chr6	43511832	43516985	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-6747-3p	chr11	62567011	62567031	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
LINC02539	chr6	137730170	137792835	-

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.