exRNAdisease

General Information

Database ID:

exR0000295

RNA Name:

ADD1

RNA Type:

mRNA

Chromosome:

chr4

Starnd:

Coordinate:

Start Site(bp):

2843857

End Site(bp):

2930076

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
HIRA	chr22	19330698	19447450	-
DDX17	chr22	38483438	38507660	-
HNRNPAB	chr5	178204533	178211163	+
ENO1	chr1	8861000	8879190	-
MFSD14A	chr1	100038095	100083377	+
RABGAP1L	chr1	174159410	174995308	+
MARCKSL1	chr1	32333839	32336233	-
MTERF4	chr2	241072169	241102332	-
EIF3L	chr22	37848868	37889407	+
CDC123	chr10	12195965	12250589	+
RPS10	chr6	34417454	34426069	-
PDHA2	chr4	95840093	95841464	+
RPL9	chr4	39452521	39458949	-
NPM1	chr5	171387116	171411137	+
IFI44L	chr1	78619922	78646145	+
SAMD11	chr1	923928	944581	+
B2M	chr15	44711487	44718877	+
POLE	chr12	132623753	132687376	-
HNRNPUL2	chr11	62712630	62727457	-
ELOC	chr8	73939169	73972287	-
RGL2	chr6	33291654	33298942	-
BIRC2	chr11	102347211	102378670	+
HLA-A	chr6	29941260	29945884	+
RPL4	chr15	66498015	66524532	-
RPS3	chr11	75399515	75422280	+
LPCAT3	chr12	6976185	7018477	-
CARHSP1	chr16	8852942	8869012	-
CAPN15	chr16	527712	554636	+
CLN6	chr15	68206992	68257211	-
RPS27A	chr2	55231903	55235853	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-184	chr15	79209840	79209861	+
hsa-miR-654-5p	chr14	101040234	101040255	+
hsa-miR-193a-5p	chr17	31560016	31560037	+
hsa-miR-361-3p	chrX	85903641	85903663	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
ACVR2B-AS1	chr3	38451027	38454820	-
AD000090.1	chr19	35557956	35581954	+
AL022311.1	chr22	37876148	37895563	+
AC009163.4	chr16	75458252	75460017	-

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.