exRNAdisease

General Information

Database ID:

exR0006262

RNA Name:

HDGF

RNA Type:

mRNA

Chromosome:

chr1

Starnd:

Coordinate:

Start Site(bp):

156742109

End Site(bp):

156766925

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	-
ABL1	chr9	130713016	130887675	+
AC006030.1	chr2	74211604	74363377	-
AC006064.6	chr12	6556886	6607367	-
AC008982.1	chr19	38817471	38840178	-
AC010422.3	chr19	12643831	12648397	-
AC093525.2	chr16	2496032	2520218	+
AC124312.1	chr15	24955034	25000276	+
AC139530.2	chr17	81703371	81720539	+
ACTB	chr7	5527148	5563784	-
ADAR	chr1	154582057	154628013	-
ADD2	chr2	70607618	70768225	-
ADD3	chr10	109996368	110135565	+
ADNP	chr20	50888916	50931437	-
AHCYL1	chr1	109984765	110023742	+
AIF1L	chr9	131096476	131123152	+
AKIRIN2	chr6	87674860	87702233	-
AKR1A1	chr1	45550543	45570049	+
AL136454.1	chr1	192716132	192716653	+
AL139011.2	chr1	160216800	160285130	-
AL590132.1	chr1	210858125	211134146	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-103a-3p	chr5	168560904	168560926	-
hsa-miR-107	chr10	89592756	89592778	-
hsa-miR-214-3p	chr1	172138816	172138837	-
hsa-miR-15b-5p	chr3	160404607	160404628	+
hsa-miR-491-5p	chr9	20716120	20716141	+
hsa-miR-873-5p	chr9	28888925	28888945	-
hsa-miR-1286	chr22	20249145	20249165	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC005083.1	chr7	20217577	20221700	+
AC016876.2	chr17	7581964	7584086	-
AC021078.1	chr5	149494314	149504670	-
AC026362.1	chr12	122975320	122982907	+
AC069281.2	chr7	100572232	100578700	-
AC079781.5	chr7	97851688	97972985	-
AC105036.3	chr15	75527150	75601205	-
AC245014.3	chr1	145281116	145281462	+
AD000090.1	chr19	35557956	35581954	+
AL022311.1	chr22	37876148	37895563	+

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.