exRNAdisease

General Information

Database ID:

exR0000476

RNA Name:

ALDH16A1

RNA Type:

mRNA

Chromosome:

chr19

Starnd:

Coordinate:

Start Site(bp):

49453225

End Site(bp):

49471050

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
MED22	chr9	133338312	133348131	-
SOX4	chr6	21593751	21598619	+
SLC52A2	chr8	144354135	144361272	+
LARGE2	chr11	45921621	45929096	+
EEF1A1	chr6	73515750	73523797	-
FASTK	chr7	151076593	151080866	-
FAT1	chr4	186587794	186726722	-
LGALS9	chr17	27629798	27649560	+
PPP1R10	chr6	30600413	30618612	-
GRB10	chr7	50590063	50793462	-
ATP6V1G2-DDX39B	chr6	31530219	31546608	-
SLC25A11	chr17	4937130	4940053	-
GSPT1	chr16	11868128	11916082	-
HOXB3	chr17	48548870	48604912	-
THOP1	chr19	2785503	2815807	+
CYB5B	chr16	69424619	69466264	+
ARFGAP1	chr20	63272785	63289790	+
CBX6	chr22	38861422	38872249	-
CTNNA1	chr5	138610967	138935034	+
B3GALT6	chr1	1232237	1235041	+
ADAMTS1	chr21	26835755	26845409	-
DHX36	chr3	154272546	154324487	-
ISG20L2	chr1	156721891	156728799	-
CDC34	chr19	531760	542092	+
ZNRF2	chr7	30284597	30367689	+
BCR	chr22	23179704	23318037	+
EEF2	chr19	3976056	3985463	-
RBM15	chr1	110338506	110346681	+
GPATCH2L	chr14	76151916	76254342	+
DDX39B	chr6	31530219	31542448	-

miRNA targets:

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC020928.2	chr19	36773712	36775908	-
AC067852.1	chr17	42536510	42562062	+
AC132217.1	chr11	2129121	2129964	-
VPS9D1-AS1	chr16	89711856	89718165	+

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.