exRNAdisease

General Information

Database ID:

exR0004317

RNA Name:

EEF1D

RNA Type:

mRNA

Chromosome:

chr8

Starnd:

Coordinate:

Start Site(bp):

143579697

End Site(bp):

143599541

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
AAMP	chr2	218264123	218270257	-
ABCA2	chr9	137007234	137028922	-
ABCC5	chr3	183919934	184017939	-
ABHD10	chr3	111979010	111993368	+
AC012184.2	chr16	70299194	70372582	+
AC074143.1	chr16	67163385	67165815	+
AC090004.1	chr3	14135217	14148252	+
AC092143.1	chr16	89919165	89936092	+
AC092647.5	chr7	55887277	55955239	+
AC093525.2	chr16	2496032	2520218	+
AC244197.3	chrX	149477104	149540926	-
AC245033.1	chr15	82536788	82573194	-
ACLY	chr17	41866917	41930542	-
ACTA1	chr1	229431245	229434098	-
ACTB	chr7	5527148	5563784	-
ACTC1	chr15	34790230	34795549	-
ACTG1	chr17	81509971	81523847	-
ACTR3	chr2	113890063	113962596	+
ADGRE5	chr19	14380501	14408725	+
AFMID	chr17	78187317	78207701	+
AHCYL2	chr7	129225023	129430211	+
AL713999.1	chr1	155169409	155187272	-
ALDH9A1	chr1	165662216	165698863	-
ALDOA	chr16	30064164	30070457	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-4517	chr16	28958587	28958611	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC067930.1	chr8	143579636	143580670	+
AC069281.2	chr7	100572232	100578700	-
AC245033.4	chr15	82533175	82540008	-
AD000090.1	chr19	35557956	35581954	+
AL132780.1	chr14	22929607	22956374	+
AL133166.1	chr14	29210986	29392048	-

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.