exRNAdisease

General Information

Database ID:

exR0000339

RNA Name:

ADSL

RNA Type:

mRNA

Chromosome:

chr22

Starnd:

Coordinate:

Start Site(bp):

40346500

End Site(bp):

40390463

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
MADD	chr11	47269161	47330031	+
HDGFL3	chr15	83112738	83207823	-
CLTC	chr17	59619689	59696956	+
MTRNR2L10	chrX	55181392	55182442	-
HNRNPR	chr1	23303771	23344336	-
TOMM7	chr7	22812628	22822852	-
MAPK6	chr15	51952106	52067375	+
STK11	chr19	1177558	1228431	+
SAP30	chr4	173369969	173377532	+
PPIAL4F	chr1	144592868	144593652	+
SND1	chr7	127652194	128092609	+
PPP1R18	chr6	30676389	30687895	-
BAG6	chr6	31639028	31652705	-
PSMD4	chr1	151254703	151267479	+
AHCY	chr20	34280268	34311802	-
AC104452.1	chr3	49416777	49429314	-
NICN1	chr3	49422946	49429326	-
ERG28	chr14	75649791	75660876	-
SGSM3	chr22	40370591	40410289	+
PFN2	chr3	149964904	150050788	-
RPS27A	chr2	55231903	55235853	+
TPM3	chr1	154155304	154194648	-
PHF19	chr9	120855651	120894896	-
ZNF20	chr19	12092843	12140355	-
PCCA	chr13	100089015	100530437	+
GIPC1	chr19	14477760	14496149	-
EEF1A1	chr6	73515750	73523797	-
DNAJA3	chr16	4425805	4456775	+
EZR	chr6	158765741	158819368	-
SLC25A17	chr22	40769630	40819399	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-193a-5p	chr17	31560016	31560037	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AL031595.3	chr22	44139365	44153626	+
AL050341.2	chr1	40256427	40257967	-
AL139819.1	chr10	100335563	100346390	-
AL353759.1	chr6	26160765	26172802	-
MIR205HG	chr1	209428817	209432838	+
NFYC-AS1	chr1	40690380	40692066	-
SNHG25	chr17	64145970	64146476	+
XIST	chrX	73820649	73852723	-

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.