exRNAdisease

General Information

Database ID:

exR0000214

RNA Name:

ACVR1B

RNA Type:

mRNA

Chromosome:

chr12

Starnd:

Coordinate:

Start Site(bp):

51951699

End Site(bp):

51997078

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
HIBADH	chr7	27525442	27662883	-
LRRC42	chr1	53946085	53968168	+
SNURF	chr15	24954986	24977850	+
RPL5	chr1	92832013	92841924	+
WDR62	chr19	36054881	36105108	+
RANBP2	chr2	108719482	108785809	+
SLC7A6	chr16	68264516	68301823	+
RPL18	chr19	48615328	48619184	-
C9orf64	chr9	83938311	83956986	-
ST6GAL1	chr3	186930502	187078553	+
PPFIA4	chr1	203026498	203078740	+
ZNF592	chr15	84748592	84806445	+
TSPAN6	chrX	100627108	100639991	-
MFGE8	chr15	88898683	88913381	-
BAZ2A	chr12	56595596	56636816	-
DGAT1	chr8	144314584	144326910	-
FZD3	chr8	28494205	28574267	+
SMG5	chr1	156249224	156282825	-
NMT1	chr17	45051610	45109016	+
SETD2	chr3	47016429	47163967	-
HACD3	chr15	65530418	65578349	+
TAOK2	chr16	29973868	29992261	+
CNPY3	chr6	42929192	42939294	+
ABCB6	chr2	219209772	219218994	-
RPL26	chr17	8377516	8383213	-
DUSP3	chr17	43766125	43778977	-
SYNGR2	chr17	78168558	78173527	+
SSBP4	chr19	18418864	18434562	+
AC010422.3	chr19	12643831	12648397	-
PCNT	chr21	46324141	46445769	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-7-5p	chr19	4770700	4770723	+
hsa-miR-143-3p	chr5	149428978	149428998	+
hsa-miR-9-5p	chr5	88666902	88666924	-
hsa-miR-136-5p	chr14	100884716	100884738	+
hsa-miR-185-5p	chr22	20033153	20033174	+
hsa-miR-342-3p	chr14	100109715	100109737	+
hsa-miR-769-5p	chr19	46018961	46018982	+
hsa-miR-541-3p	chr14	101064548	101064569	+
hsa-miR-760	chr1	93846880	93846899	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC139149.1	chr17	81514047	81527776	+
AD000090.1	chr19	35557956	35581954	+
AC135178.2	chr17	8318088	8318712	-
DANCR	chr4	52712404	52720351	+
NEAT1	chr11	65422774	65445540	+
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.