exRNAdisease

General Information

Database ID:

exR0004419

RNA Name:

EIF4B

RNA Type:

mRNA

Chromosome:

chr12

Starnd:

Coordinate:

Start Site(bp):

53006158

End Site(bp):

53042209

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	-
AC008763.3	chr19	7678501	7682854	+
AC010422.3	chr19	12643831	12648397	-
AC011462.1	chr19	41350853	41425001	+
AC058822.1	chr4	53377839	54295272	+
AC073508.2	chr17	40627356	40665141	-
AC093525.1	chr16	2513965	2527955	+
AC124312.1	chr15	24955034	25000276	+
AC245033.1	chr15	82536788	82573194	-
ACADVL	chr17	7217125	7225266	+
ACOT8	chr20	45841721	45857405	-
ACSF2	chr17	50426158	50474845	+
ACTB	chr7	5527148	5563784	-
ACTG1	chr17	81509971	81523847	-
ACVR1	chr2	157736444	157876330	-
ADAL	chr15	43330657	43354555	+
ADAR	chr1	154582057	154628013	-
ADIPOR2	chr12	1688574	1788674	+
ADORA2A	chr22	24417879	24442357	+
AEN	chr15	88621337	88632281	+
AGBL5	chr2	27042364	27070622	+
AHCY	chr20	34280268	34311802	-
AIG1	chr6	143060496	143341058	+
AIMP1	chr4	106315544	106349456	+
AKNA	chr9	114334156	114394405	-
AL121594.1	chr14	35122549	35317474	+
AL139011.2	chr1	160216800	160285130	-
ALDOA	chr16	30064164	30070457	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-3680-5p	chr16	21506101	21506122	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC018647.2	chr7	35695214	35699413	+
AC023509.1	chr12	53441741	53467528	+
AC245033.4	chr15	82533175	82540008	-
AD000090.1	chr19	35557956	35581954	+
AL022311.1	chr22	37876148	37895563	+
AL118506.1	chr20	63861212	63864293	-
AL121832.3	chr20	62402236	62405935	-

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.