exRNAdisease

General Information

Database ID:

exR0001520

RNA Name:

BSG

RNA Type:

mRNA

Chromosome:

chr19

Starnd:

Coordinate:

Start Site(bp):

571277

End Site(bp):

583493

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
ABCC1	chr16	15949577	16143074	+
ABCC5	chr3	183919934	184017939	-
ABCF1	chr6	30571393	30597179	+
AC005258.1	chr19	2269525	2341172	+
AC010422.3	chr19	12643831	12648397	-
AC011005.1	chr7	129126518	129130793	+
AC012531.3	chr12	53985845	54034888	+
AC058822.1	chr4	53377839	54295272	+
AC104109.3	chr5	134167170	134226071	-
AC245033.1	chr15	82536788	82573194	-
ACBD4	chr17	45132600	45144181	+
ACO2	chr22	41469117	41528989	+
ACTB	chr7	5527148	5563784	-
ACVR2B	chr3	38453890	38493142	+
ADH5	chr4	99070978	99088801	-
ADPRHL2	chr1	36088892	36093932	+
ADRA1D	chr20	4220630	4249287	-
AGAP3	chr7	151085831	151144436	+
AGAP4	chr10	45825594	45853875	-
AGFG1	chr2	227472152	227561214	+
AGPAT4	chr6	161129967	161274061	-
AHCY	chr20	34280268	34311802	-
AHNAK	chr11	62433542	62556235	-
AKAP17A	chrX	1591604	1602520	+
AKT1	chr14	104769349	104795751	-
AL133352.1	chr10	100505628	100529881	-
AL139353.1	chr14	31334312	31457441	-
ALDOA	chr16	30064164	30070457	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-664b-5p	chrX	154768596	154768619	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC007161.3	chr7	7640752	8004053	+
AC007952.4	chr17	19112000	19112636	-
AC012531.2	chr12	54017110	54035361	+
AC124068.2	chr15	89335053	89336161	+
AC245033.4	chr15	82533175	82540008	-
AD000090.1	chr19	35557956	35581954	+
AL035458.2	chr20	34234840	34281173	-

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.