exRNAdisease

General Information

Database ID:

exR0000303

RNA Name:

ADH5

RNA Type:

mRNA

Chromosome:

chr4

Starnd:

Coordinate:

Start Site(bp):

99070978

End Site(bp):

99088801

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
GALNT2	chr1	230057990	230282122	+
CLPTM1	chr19	44954585	44993341	+
BUB1B	chr15	40161023	40221136	+
MAD1L1	chr7	1815793	2233243	-
PSAP	chr10	71816298	71851325	-
RSAD1	chr17	50478860	50485974	+
PTPN6	chr12	6946468	6961316	+
ACTR6	chr12	100199122	100241865	+
SRP68	chr17	76038775	76072517	-
CEBPZ	chr2	37201612	37231596	-
SEC61A1	chr3	128051641	128071683	+
TYRO3	chr15	41557675	41583589	+
RPS19	chr19	41860255	41872925	+
SMARCA4	chr19	10960825	11079426	+
ILF2	chr1	153661788	153671028	-
NUDCD3	chr7	44379119	44490658	-
SEC22A	chr3	123201927	123274136	+
RAN	chr12	130872037	130877678	+
OTX2	chr14	56799905	56816693	-
RPL15	chr3	23916545	23924374	+
SLX1A	chr16	30193887	30197561	+
C5orf30	chr5	103258763	103278660	+
TUBB	chr6	30720352	30725426	+
WDFY1	chr2	223855716	223945357	-
AL136454.1	chr1	192716132	192716653	+
VIM	chr10	17228241	17237593	+
TAF6	chr7	100107070	100119841	-
HMGA1	chr6	34236873	34246231	+
PABPC1	chr8	100685816	100722809	-
VCL	chr10	73995193	74121363	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-1825	chr20	32237830	32237847	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
C5orf17	chr5	23951348	24178263	+
OXCT1-AS1	chr5	41869927	41872241	+
SLX1A-SULT1A3	chr16	30193892	30204310	+
SNHG15	chr7	44983023	44986961	-
TUG1	chr22	30969245	30979395	+

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.