exRNAdisease

General Information

Database ID:

exR0005400

RNA Name:

FUS

RNA Type:

mRNA

Chromosome:

chr16

Starnd:

Coordinate:

Start Site(bp):

31180110

End Site(bp):

31194871

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
AAGAB	chr15	67200667	67255195	-
ACTN4	chr19	38647649	38731589	+
ADCY6	chr12	48766194	48789037	-
AC091167.2	chr15	90249556	90272208	+
AC007192.1	chr19	18153158	18178117	+
AHCY	chr20	34280268	34311802	-
AAMP	chr2	218264123	218270257	-
AC010422.3	chr19	12643831	12648397	-
ABRACL	chr6	139028745	139043302	+
ACTR2	chr2	65227753	65271253	+
AC093525.1	chr16	2513965	2527955	+
AFDN	chr6	167826922	167972023	+
AL365205.1	chr6	41780349	41790141	+
AEBP2	chr12	19404045	19720801	+
AC093525.2	chr16	2496032	2520218	+
ACTR5	chr20	38748460	38772520	+
ACTB	chr7	5527148	5563784	-
AL359736.1	chr13	23979700	24321031	+
AC005832.4	chr12	4604944	4662643	+
AKT1S1	chr19	49869033	49878459	-
AC092143.1	chr16	89919165	89936092	+
ALDH4A1	chr1	18871430	18902724	-
ADGRL2	chr1	81306160	81992436	+
AC004922.1	chr7	99325879	99394653	+
ALDOA	chr16	30064164	30070457	+
AGTRAP	chr1	11736084	11754802	+
AC008878.3	chr19	7382834	7470241	+
AC138811.2	chr16	18788063	18801519	-
ACTG1	chr17	81509971	81523847	-
AKR7A2	chr1	19303965	19312146	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-221-3p	chrX	45746180	45746202	-
hsa-miR-4508	chr15	23562107	23562123	-
hsa-miR-4521	chr17	8186948	8186969	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC005726.3	chr17	28573117	28574243	+
AC020928.2	chr19	36773712	36775908	-
AC023509.1	chr12	53441741	53467528	+
AC079781.5	chr7	97851688	97972985	-
AC096992.2	chr3	136837338	136839021	-
AC245014.3	chr1	145281116	145281462	+
AD000090.1	chr19	35557956	35581954	+
AL022311.1	chr22	37876148	37895563	+
AL031282.2	chr1	1702736	1737688	-

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.