exRNAdisease

General Information

Database ID:

exR0000203

RNA Name:

ACTR1B

RNA Type:

mRNA

Chromosome:

chr2

Starnd:

Coordinate:

Start Site(bp):

97655939

End Site(bp):

97664044

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
TEDC2	chr16	2460086	2464963	+
COMMD1	chr2	61888724	62147247	+
SDC2	chr8	96493813	96611790	+
SND1	chr7	127652194	128092609	+
RAB11A	chr15	65726054	65891989	+
ACTG1	chr17	81509971	81523847	-
PCBP1	chr2	70087477	70089203	+
WRAP73	chr1	3630767	3652761	-
ACTA1	chr1	229431245	229434098	-
SNURF	chr15	24954986	24977850	+
PIK3C2B	chr1	204422628	204494724	-
KEAP1	chr19	10486125	10503558	-
GAPDH	chr12	6534512	6538374	+
GSTP1	chr11	67583742	67586656	+
POTEE	chr2	131218067	131265278	+
KCTD2	chr17	75032575	75065889	+
YLPM1	chr14	74763316	74859435	+
MTRNR2L12	chr3	96617188	96618236	-
MFSD2B	chr2	24010081	24063321	+
PGAM1	chr10	97426191	97433444	+
BAG6	chr6	31639028	31652705	-
PTMA	chr2	231706895	231713541	+
PSMB1	chr6	170535120	170553307	-
PLXNB2	chr22	50274979	50307646	-
RPN1	chr3	128619969	128681075	-
ZNF106	chr15	42412823	42491141	-
CLNS1A	chr11	77514936	77637794	-
ABLIM1	chr10	114431113	114768061	-
AL136295.5	chr14	24147548	24166452	+
EWSR1	chr22	29268009	29300525	+

miRNA targets:

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC008555.1	chr19	34811589	34814345	-
AL021707.2	chr22	38667585	38681847	-
AL355075.4	chr14	20343048	20343685	-

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.