exRNAdisease

General Information

Database ID:

exR0000185

RNA Name:

ACTA2

RNA Type:

mRNA

Chromosome:

chr10

Starnd:

Coordinate:

Start Site(bp):

88935074

End Site(bp):

88991339

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
ZNF516	chr18	76357682	76495242	-
HNRNPDL	chr4	82422564	82430408	-
RPS16	chr19	39433137	39435949	-
HLA-B	chr6	31269491	31357188	-
ATP5F1B	chr12	56638175	56645984	-
TMSB4X	chrX	12975110	12977227	+
HLA-A	chr6	29941260	29945884	+
POTEF	chr2	130073535	130129222	-
GCN1	chr12	120127202	120194715	-
HNRNPH3	chr10	68331174	68343191	+
TRAP1	chr16	3651639	3717553	-
ATP5PB	chr1	111448864	111462773	+
PWWP2B	chr10	132397168	132417859	+
PHF23	chr17	7235029	7239722	-
HLA-DMA	chr6	32948613	32969094	-
RPS8	chr1	44775251	44778779	+
PEX2	chr8	76980258	77001044	-
BAIAP2L1	chr7	98291650	98401090	-
CLUH	chr17	2689386	2712663	-
UQCRC1	chr3	48599002	48610976	-
CCT7	chr2	73233420	73253021	+
HLA-DQA1	chr6	32628179	32647062	+
ACTG1	chr17	81509971	81523847	-
CNBP	chr3	129169484	129183922	-
PTTG1	chr5	160421855	160428739	+
ATN1	chr12	6924463	6942321	+
DDIT4	chr10	72273924	72276036	+
POLN	chr4	2071918	2242121	-
RAB12	chr18	8609437	8639382	+
RARA	chr17	40309180	40357643	+

miRNA targets:

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC139149.1	chr17	81514047	81527776	+
AC013269.1	chr2	130530275	130537182	+
MALAT1	chr11	65497688	65506516	+
NEAT1	chr11	65422774	65445540	+

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.