exRNAdisease

General Information

Database ID:

exR0000017

RNA Name:

AAR2

RNA Type:

mRNA

Chromosome:

chr20

Starnd:

Coordinate:

Start Site(bp):

36236459

End Site(bp):

36270918

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
MCM3AP	chr21	46235133	46286297	-
PLCB2	chr15	40278176	40307935	-
MANBAL	chr20	37289638	37317260	+
LDHA	chr11	18394560	18408425	+
DHX15	chr4	24517441	24584554	-
YWHAH	chr22	31944522	31957603	+
M6PR	chr12	8940361	8949761	-
LSS	chr21	46188141	46228824	-
MTHFR	chr1	11785723	11806455	-
EGLN2	chr19	40798996	40808434	+
COX6B1	chr19	35648323	35658782	+
PKP2	chr12	32790745	32896840	-
TEN1-CDK3	chr17	75979231	76005999	+
TMEM47	chrX	34627075	34657285	-
HMOX2	chr16	4474690	4510347	+
BRF1	chr14	105209286	105315589	-
CCDC77	chr12	389273	442642	+
DDX17	chr22	38483438	38507660	-
NELFE	chr6	31952087	31959038	-
PAGR1	chr16	29816152	29822489	+
LMTK2	chr7	98106862	98209638	+
RAB4B-EGLN2	chr19	40778242	40808418	+
HNRNPH3	chr10	68331174	68343191	+
ACTR1A	chr10	102461881	102502712	-
CANX	chr5	179678628	179731641	+
MCM7	chr7	100092728	100101940	-
RPL3	chr22	39312882	39320389	-
FLII	chr17	18244815	18258738	-
TUBA1A	chr12	49184795	49189080	-
PAICS	chr4	56435741	56464579	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-103a-3p	chr5	168560904	168560926	-
hsa-miR-147a	chr9	120244985	120245004	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
EBLN3P	chr9	37079645	37090928	+

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.