exRNAdisease

General Information

Database ID:

exR0000382

RNA Name:

AGPAT3

RNA Type:

mRNA

Chromosome:

chr21

Starnd:

Coordinate:

Start Site(bp):

43865223

End Site(bp):

43987592

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
TUBB	chr6	30720352	30725426	+
WDR54	chr2	74421678	74425755	+
RPLP1	chr15	69452814	69456205	+
CARD9	chr9	136361903	136373681	-
VAPB	chr20	58389229	58451101	+
IPO9	chr1	201829149	201884291	+
KCTD3	chr1	215567304	215621807	+
IMP3	chr15	75639085	75648706	-
CLN3	chr16	28474111	28495575	-
OSGEP	chr14	20446401	20455089	-
PPRC1	chr10	102132994	102150333	+
CKLF	chr16	66552563	66566251	+
PDIA4	chr7	149003062	149028662	-
RBM15	chr1	110338506	110346681	+
RPL27A	chr11	8682788	8714759	+
ANKRD28	chr3	15667236	15859771	-
HLA-B	chr6	31269491	31357188	-
BHLHE40	chr3	4979437	4985323	+
SQSTM1	chr5	179806398	179838078	+
RER1	chr1	2391775	2405442	+
LAMC1	chr1	183023420	183145592	+
RUNDC1	chr17	42980565	42993690	+
POMK	chr8	43093506	43123434	+
GON4L	chr1	155749662	155859400	-
ACAP3	chr1	1292390	1309609	-
DTNBP1	chr6	15522801	15663058	-
PIK3R2	chr19	18153163	18170532	+
ACIN1	chr14	23058564	23095614	-
AC007192.1	chr19	18153158	18178117	+
SPC24	chr19	11131520	11155808	-

miRNA targets:

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AL049840.4	chr14	103694516	103695050	-
AC010326.4	chr19	57867038	57868172	-
AL355075.4	chr14	20343048	20343685	-
LINC00665	chr19	36313067	36331770	-
LINC01754	chr20	47391925	47412327	-

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.