exRNAdisease

General Information

Database ID:

exR0012427

RNA Name:

RPS8

RNA Type:

mRNA

Chromosome:

chr1

Starnd:

Coordinate:

Start Site(bp):

44775251

End Site(bp):

44778779

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
ACVR1B	chr12	51951699	51997078	+
AL021546.1	chr12	120438198	120460006	+
AC073508.2	chr17	40627356	40665141	-
AC008758.1	chr19	12461559	12551474	-
ACAT1	chr11	108116695	108147603	+
AC120057.2	chr17	7240427	7244635	-
AC138811.2	chr16	18788063	18801519	-
ADNP	chr20	50888916	50931437	-
AHCYL1	chr1	109984765	110023742	+
AGL	chr1	99850361	99924023	+
ABI3	chr17	49210411	49223225	+
ACTG1	chr17	81509971	81523847	-
ACTR1B	chr2	97655939	97664044	-
ACTA2	chr10	88935074	88991339	-
AL136295.5	chr14	24147548	24166452	+
ABRACL	chr6	139028745	139043302	+
AKIRIN1	chr1	38991276	39006059	+
AKT1	chr14	104769349	104795751	-
ACTA1	chr1	229431245	229434098	-
AL669918.1	chr6	32813767	32838822	-
AHRR	chr5	271670	438291	+
ABCD4	chr14	74285269	74303055	-
AGPAT3	chr21	43865223	43987592	+
AEN	chr15	88621337	88632281	+
AC002985.1	chr19	18907013	18934397	-
AKR7A2	chr1	19303965	19312146	-
ADRM1	chr20	62302093	62308862	+
AC022384.1	chr3	10249372	10285796	+
ADAR	chr1	154582057	154628013	-
ADD1	chr4	2843857	2930076	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-92a-3p	chrX	134169544	134169565	-
hsa-miR-367-3p	chr4	112647877	112647898	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC063949.2	chr12	92421531	92483680	+
AC090772.3	chr18	24159509	24162211	-

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.