exRNAdisease

General Information

Database ID:

exR0004407

RNA Name:

EIF3E

RNA Type:

mRNA

Chromosome:

chr8

Starnd:

Coordinate:

Start Site(bp):

108201216

End Site(bp):

108435333

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
ABLIM1	chr10	114431113	114768061	-
AC008764.4	chr19	16577642	16660115	-
AC009133.6	chr16	29812261	29820092	+
AC012184.2	chr16	70299194	70372582	+
AC048338.1	chr12	122207779	122266423	-
AC079447.1	chr2	99141485	99322741	+
AC092587.1	chr2	99154998	99195298	+
AC104452.1	chr3	49416777	49429314	-
AC120057.2	chr17	7240427	7244635	-
ACTB	chr7	5527148	5563784	-
ADK	chr10	74151202	74709963	+
AHCY	chr20	34280268	34311802	-
AL136454.1	chr1	192716132	192716653	+
ALCAM	chr3	105366909	105576900	+
ALDH1B1	chr9	38392702	38398661	+
ALDH5A1	chr6	24494867	24537207	+
ALDOA	chr16	30064164	30070457	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-93-5p	chr7	100093815	100093837	-
hsa-miR-4284	chr7	73711327	73711344	+
hsa-miR-4426	chr1	192716333	192716349	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC010618.3	chr19	17488990	17511889	-
AC021078.1	chr5	149494314	149504670	-
AC124312.5	chr15	25091786	25107469	-
AC132217.1	chr11	2129121	2129964	-
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.