exRNAdisease

General Information

Database ID:

exR0012429

RNA Name:

RPSA

RNA Type:

mRNA

Chromosome:

chr3

Starnd:

Coordinate:

Start Site(bp):

39406716

End Site(bp):

39412542

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
ABHD12	chr20	25294742	25390835	-
ABHD2	chr15	89087459	89202355	+
AC008575.1	chr5	112827213	112867582	+
AC018523.2	chr11	14493783	14520344	-
AC104109.3	chr5	134167170	134226071	-
ACACA	chr17	37084992	37406836	-
ACSL6	chr5	131949973	132012243	-
ACTA2	chr10	88935074	88991339	-
ACTB	chr7	5527148	5563784	-
ACTG1	chr17	81509971	81523847	-
AFF4	chr5	132875395	132963634	-
AGFG1	chr2	227472152	227561214	+
AHCY	chr20	34280268	34311802	-
AL355987.3	chr9	136791379	136800595	+
ALDH7A1	chr5	126531200	126595362	-

miRNA targets:

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC004687.1	chr17	58330884	58332508	-
AC005618.1	chr5	141326210	141329357	+
AC005899.4	chr17	32328441	32329395	+
AC006064.5	chr12	6510275	6510522	+
AC016876.2	chr17	7581964	7584086	-
AC019205.1	chr6	73263212	73301789	+
AC023509.1	chr12	53441741	53467528	+
AC068205.2	chr11	43578889	43840030	+
AC087190.3	chr16	9104848	9113181	+
AC091564.7	chr11	6610883	6616594	-
AC124312.3	chr15	25087661	25088896	+
AC132217.1	chr11	2129121	2129964	-
AD000090.1	chr19	35557956	35581954	+

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.