exRNAdisease

General Information

Database ID:

exR0003422

RNA Name:

CTNNA1

RNA Type:

mRNA

Chromosome:

chr5

Starnd:

Coordinate:

Start Site(bp):

138610967

End Site(bp):

138935034

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
AAK1	chr2	69457997	69674349	-
AAMP	chr2	218264123	218270257	-
AC011455.2	chr19	38915404	38949855	-
AC099811.2	chr17	42119674	42154916	-
ACIN1	chr14	23058564	23095614	-
ACSL3	chr2	222860942	222944639	+
ACTG1	chr17	81509971	81523847	-
ACTN4	chr19	38647649	38731589	+
ADA2	chr22	17178790	17258235	-
ADARB1	chr21	45073853	45226560	+
ADD3	chr10	109996368	110135565	+
ADH5	chr4	99070978	99088801	-
ADNP	chr20	50888916	50931437	-
ADNP2	chr18	80109262	80147523	+
ADSL	chr22	40346500	40390463	+
AGPAT1	chr6	32168212	32178096	-
AIG1	chr6	143060496	143341058	+
AKAP8	chr19	15353385	15379798	-
AL022238.4	chr22	40346529	40410054	+
AL603832.3	chr1	112702614	112711433	-
ALDH16A1	chr19	49453225	49471050	+
ALDH2	chr12	111766887	111817532	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-320a-3p	chr8	22244975	22244996	-
hsa-miR-7705	chr8	100703002	100703024	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC007405.3	chr2	170814686	170818037	-
AC018521.1	chr17	47945424	47981736	+
AC026304.1	chr3	143000907	143001467	-
AC092490.1	chr12	8788253	8795789	+
AC138035.1	chr5	181306502	181324685	+

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.