exRNAdisease

General Information

Database ID:

exR0012403

RNA Name:

RPS25

RNA Type:

mRNA

Chromosome:

chr11

Starnd:

Coordinate:

Start Site(bp):

119015712

End Site(bp):

119018691

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
ABI2	chr2	203328239	203447728	+
AC004922.1	chr7	99325879	99394653	+
AC091167.2	chr15	90249556	90272208	+
AC092647.5	chr7	55887277	55955239	+
ACAD9	chr3	128879596	128916067	+
ACSS3	chr12	80936414	81261210	+
ACTA1	chr1	229431245	229434098	-
ACTB	chr7	5527148	5563784	-
ACTG1	chr17	81509971	81523847	-
ADCK2	chr7	140672945	140696261	+
ADCY3	chr2	24819169	24919839	-
ADD1	chr4	2843857	2930076	+
ADD3	chr10	109996368	110135565	+
ADPRH	chr3	119579268	119589945	+
AFG3L2	chr18	12328944	12377227	-
AGFG1	chr2	227472152	227561214	+
AGK	chr7	141551278	141655244	+
AGPAT3	chr21	43865223	43987592	+
AICDA	chr12	8602170	8612867	-
AKAP13	chr15	85380571	85749358	+
AKAP17A	chrX	1591604	1602520	+
ALDOA	chr16	30064164	30070457	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-1248	chr3	186786675	186786701	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC026362.1	chr12	122975320	122982907	+
AC026464.2	chr16	69463844	69466264	+
AC121761.2	chr12	75333798	75334486	-
AC126365.1	chr17	20788071	20789584	+
AC132217.1	chr11	2129121	2129964	-
AD000090.1	chr19	35557956	35581954	+
AL021707.1	chr22	38739003	38749041	+

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.