exRNAdisease

General Information

Database ID:

exR0000205

RNA Name:

ACTR3

RNA Type:

mRNA

Chromosome:

chr2

Starnd:

Coordinate:

Start Site(bp):

113890063

End Site(bp):

113962596

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
CD53	chr1	110871188	110899922	+
PTPRCAP	chr11	67435510	67437682	-
GLI1	chr12	57459785	57472268	+
MT-ATP6	chrMT	8527	9207	+
EZR	chr6	158765741	158819368	-
PGRMC2	chr4	128269237	128288829	-
RPL11	chr1	23691742	23696835	+
TRIM27	chr6	28903002	28923988	-
RPL4	chr15	66498015	66524532	-
TEAD3	chr6	35473597	35497079	-
ERLIN1	chr10	100150094	100186033	-
SF3A1	chr22	30331988	30356919	-
MARS2	chr2	197705369	197708395	+
AC245033.1	chr15	82536788	82573194	-
CENPI	chrX	101098218	101163681	+
ERG28	chr14	75649791	75660876	-
PSMD8	chr19	38374536	38383824	+
NUMA1	chr11	72002864	72080693	-
DSTN	chr20	17570075	17609919	+
UBE2D3	chr4	102794383	102868896	-
TSPAN33	chr7	129144707	129169699	+
RPS29	chr14	49570984	49599164	-
DDB1	chr11	61299451	61342596	-
ERGIC3	chr20	35542021	35557634	+
CCT8	chr21	29055805	29073797	-
MLXIPL	chr7	73593194	73624543	-
HLA-DRB5	chr6	32517353	32530287	-
PCBP2	chr12	53452102	53481162	+
MEX3A	chr1	156072013	156082465	-
ATPAF1	chr1	46632737	46673867	-

miRNA targets:

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC023509.1	chr12	53441741	53467528	+
AC245033.4	chr15	82533175	82540008	-
AL035458.2	chr20	34234840	34281173	-
AC093734.1	chr7	1508655	1509427	-
GAS5	chr1	173858559	173868882	-
MALAT1	chr11	65497688	65506516	+
TMEM147-AS1	chr19	35540738	35546029	-
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.