exRNAdisease

General Information

Database ID:

exR0004316

RNA Name:

EEF1B2

RNA Type:

mRNA

Chromosome:

chr2

Starnd:

Coordinate:

Start Site(bp):

206159585

End Site(bp):

206162928

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
ABHD8	chr19	17292131	17310236	-
ABI2	chr2	203328239	203447728	+
AC005258.1	chr19	2269525	2341172	+
AC006978.2	chr7	30362400	30412502	+
AC007192.1	chr19	18153158	18178117	+
AC008763.3	chr19	7678501	7682854	+
AC009133.6	chr16	29812261	29820092	+
AC099811.2	chr17	42119674	42154916	-
AC118553.2	chr1	99970011	100083321	+
AC139530.2	chr17	81703371	81720539	+
ACAP3	chr1	1292390	1309609	-
ACTB	chr7	5527148	5563784	-
ACTG1	chr17	81509971	81523847	-
ACTG2	chr2	73892314	73919865	+
ACTN4	chr19	38647649	38731589	+
ACTR1A	chr10	102461881	102502712	-
ACTR2	chr2	65227753	65271253	+
ACTR3	chr2	113890063	113962596	+
ADAM8	chr10	133262420	133276868	-
ADSL	chr22	40346500	40390463	+
AHDC1	chr1	27534035	27604431	-
AHSA1	chr14	77457870	77469472	+
AIMP1	chr4	106315544	106349456	+
AK2	chr1	33007940	33080996	-
AL049629.2	chr11	33698261	33722467	-
ALDH4A1	chr1	18871430	18902724	-
ALDOA	chr16	30064164	30070457	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-21-5p	chr17	59841273	59841294	+
hsa-miR-6892-5p	chr7	143382686	143382706	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC004477.1	chr17	48045141	48048073	-
AC007952.4	chr17	19112000	19112636	-
AC017100.1	chr18	31685655	31686823	+
AC105339.2	chr15	82752884	82757208	+
AL022311.1	chr22	37876148	37895563	+
AL132655.2	chr20	58817132	58817725	-

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.