exRNAdisease

General Information

Database ID:

exR0006448

RNA Name:

HNRNPU

RNA Type:

mRNA

Chromosome:

chr1

Starnd:

Coordinate:

Start Site(bp):

244840638

End Site(bp):

244864560

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
ABCC4	chr13	95019835	95301475	-
AC004922.1	chr7	99325879	99394653	+
AC010422.3	chr19	12643831	12648397	-
AC012184.2	chr16	70299194	70372582	+
AC116366.3	chr5	132410832	132646079	+
AC131160.1	chr3	183815568	183884889	-
AC138811.2	chr16	18788063	18801519	-
AC140504.1	chr16	15395754	15515348	+
ACLY	chr17	41866917	41930542	-
ACSL3	chr2	222860942	222944639	+
ACTA1	chr1	229431245	229434098	-
ACTB	chr7	5527148	5563784	-
ACTG1	chr17	81509971	81523847	-
ACTR1A	chr10	102461881	102502712	-
ADARB1	chr21	45073853	45226560	+
ADD1	chr4	2843857	2930076	+
ADGRV1	chr5	90529344	91164437	+
ADPRHL2	chr1	36088892	36093932	+
AFTPH	chr2	64524305	64593005	+
AGO2	chr8	140520156	140635633	-
AGO4	chr1	35808016	35857890	+
AGRN	chr1	1020120	1056118	+
AHCY	chr20	34280268	34311802	-
AIDA	chr1	222668013	222713210	-
AKAP8L	chr19	15380050	15419141	-
AKNA	chr9	114334156	114394405	-
AL136531.2	chr20	1317571	1393096	-
AL138752.2	chr9	37588413	38068687	-
ALDH1B1	chr9	38392702	38398661	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-1244	chr2	231713368	231713393	+
hsa-miR-3654	chr7	133034860	133034878	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC010542.4	chr16	66549280	66551189	+
AC016876.2	chr17	7581964	7584086	-
AC124068.2	chr15	89335053	89336161	+
AC132217.1	chr11	2129121	2129964	-
AC245014.3	chr1	145281116	145281462	+
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.