exRNAdisease

General Information

Database ID:

exR0012096

RNA Name:

RHOA

RNA Type:

mRNA

Chromosome:

chr3

Starnd:

Coordinate:

Start Site(bp):

49359145

End Site(bp):

49412998

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
AC012254.2	chr18	47108188	47176345	-
AL603832.3	chr1	112702614	112711433	-
AKAP9	chr7	91940867	92110673	+
AC010422.3	chr19	12643831	12648397	-
AC008982.1	chr19	38817471	38840178	-
AC087289.3	chr17	75898645	75930129	-
AL928654.3	chr14	105487199	105492267	+
AC023055.1	chr12	55757275	55827546	-
ABCE1	chr4	145098288	145129524	+
ADIPOR1	chr1	202940826	202958572	-
ADAM10	chr15	58588809	58749791	-
ACAT2	chr6	159762045	159779112	+
AL022238.4	chr22	40346529	40410054	+
AC007192.1	chr19	18153158	18178117	+
AHCY	chr20	34280268	34311802	-
AC008763.3	chr19	7678501	7682854	+
ACTB	chr7	5527148	5563784	-
ADSL	chr22	40346500	40390463	+
ABHD14B	chr3	51968510	51983409	-
ACACA	chr17	37084992	37406836	-
ACIN1	chr14	23058564	23095614	-
ACTG1	chr17	81509971	81523847	-
AL590764.2	chrX	71103987	71111575	-
AC135050.2	chr16	31083439	31094956	-
ADNP2	chr18	80109262	80147523	+
AC245033.1	chr15	82536788	82573194	-
ACTL6A	chr3	179562886	179588407	+
AC027796.3	chr17	3585149	3636249	-
ADCY1	chr7	45574140	45723116	+
AK2	chr1	33007940	33080996	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-122-5p	chr18	58451088	58451109	+
hsa-miR-130b-3p	chr22	21653354	21653375	+
hsa-miR-454-3p	chr17	59137787	59137809	-
hsa-miR-1244	chr2	231713368	231713393	+
hsa-miR-4284	chr7	73711327	73711344	+
hsa-miR-4492	chr11	118910765	118910781	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC005062.1	chr7	19918981	20140453	-
AC007952.4	chr17	19112000	19112636	-
AC023509.1	chr12	53441741	53467528	+
AC073050.1	chr2	167293171	167558333	+
AC093227.1	chr19	37728586	37730643	-
AC245033.4	chr15	82533175	82540008	-
AL022311.1	chr22	37876148	37895563	+

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.