exRNAdisease

General Information

Database ID:

exR0012414

RNA Name:

RPS5

RNA Type:

mRNA

Chromosome:

chr19

Starnd:

Coordinate:

Start Site(bp):

58386400

End Site(bp):

58394806

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
AGFG2	chr7	100539203	100568220	+
AL358113.1	chr9	69035747	69255187	+
AKAP1	chr17	57085092	57121346	+
ACO2	chr22	41469117	41528989	+
AL022238.4	chr22	40346529	40410054	+
AC004832.3	chr22	30409255	30428990	+
AC007192.1	chr19	18153158	18178117	+
AC139530.2	chr17	81703371	81720539	+
AC010422.3	chr19	12643831	12648397	-
AC092073.1	chr19	34396315	34409364	+
AC040162.1	chr16	67929614	67936017	-
ABRACL	chr6	139028745	139043302	+
ACTN4	chr19	38647649	38731589	+
AHDC1	chr1	27534035	27604431	-
AHCYL1	chr1	109984765	110023742	+
AHCY	chr20	34280268	34311802	-
ACTR1B	chr2	97655939	97664044	-
ACTB	chr7	5527148	5563784	-
ALDOA	chr16	30064164	30070457	+
AK2	chr1	33007940	33080996	-
AC008763.3	chr19	7678501	7682854	+
AC002985.1	chr19	18907013	18934397	-
AC011462.1	chr19	41350853	41425001	+
ABHD10	chr3	111979010	111993368	+
AC018523.2	chr11	14493783	14520344	-
AC104452.1	chr3	49416777	49429314	-
AHSA1	chr14	77457870	77469472	+
ABCC1	chr16	15949577	16143074	+
ADSL	chr22	40346500	40390463	+
AACS	chr12	125065434	125143333	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-1244	chr2	231713368	231713393	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC026362.1	chr12	122975320	122982907	+
AC091564.7	chr11	6610883	6616594	-
AC121761.1	chr12	75483454	75489820	-
AD000090.1	chr19	35557956	35581954	+
AL121832.3	chr20	62402236	62405935	-

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.