exRNAdisease

General Information

Database ID:

exR0012412

RNA Name:

RPS4X

RNA Type:

mRNA

Chromosome:

chrX

Starnd:

Coordinate:

Start Site(bp):

72255679

End Site(bp):

72277248

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
AGPAT3	chr21	43865223	43987592	+
ALDOA	chr16	30064164	30070457	+
ACSL3	chr2	222860942	222944639	+
ADAR	chr1	154582057	154628013	-
ACAA1	chr3	38103129	38137242	-
AL022238.4	chr22	40346529	40410054	+
AL136454.1	chr1	192716132	192716653	+
ADSL	chr22	40346500	40390463	+
AKAP13	chr15	85380571	85749358	+
ADTRP	chr6	11712054	11807046	-
ADA2	chr22	17178790	17258235	-
ABCF2	chr7	151207837	151227166	-
AC026464.4	chr16	69299682	69322700	+
AC011530.1	chr19	45779437	45785973	-
AL590764.2	chrX	71103987	71111575	-
AKR1A1	chr1	45550543	45570049	+
AASS	chr7	122073549	122144255	-
AC245033.1	chr15	82536788	82573194	-
ADRM1	chr20	62302093	62308862	+
AC010422.3	chr19	12643831	12648397	-
ACAD9	chr3	128879596	128916067	+
ACKR3	chr2	236567787	236582354	+
AC010132.3	chr7	42909273	42932174	-
AC139530.2	chr17	81703371	81720539	+
ACAT1	chr11	108116695	108147603	+
AC120057.2	chr17	7240427	7244635	-
ACTB	chr7	5527148	5563784	-
ACIN1	chr14	23058564	23095614	-
AC104452.1	chr3	49416777	49429314	-
ACTG1	chr17	81509971	81523847	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-155-5p	chr21	25573983	25574006	+
hsa-miR-3651	chr9	92292461	92292484	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC006511.5	chr12	8014093	8019007	-
AC016876.2	chr17	7581964	7584086	-
AC020663.1	chr16	4730115	4752565	-
AC023509.1	chr12	53441741	53467528	+
AC087190.3	chr16	9104848	9113181	+
AC091564.7	chr11	6610883	6616594	-
AC107959.2	chr8	23068229	23083619	+
AD000090.1	chr19	35557956	35581954	+
AL022311.1	chr22	37876148	37895563	+
AL118506.1	chr20	63861212	63864293	-

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.