exRNAdisease

General Information

Database ID:

exR0000384

RNA Name:

AGPAT5

RNA Type:

mRNA

Chromosome:

chr8

Starnd:

Coordinate:

Start Site(bp):

6708642

End Site(bp):

6761503

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
MFSD14B	chr9	94374569	94461042	+
RPL18A	chr19	17859910	17864153	+
NCL	chr2	231453531	231483641	-
PFN1	chr17	4945652	4949061	-
GNA12	chr7	2728105	2844308	-
RPL14	chr3	40457292	40468587	+
MMP24OS	chr20	35201745	35278131	-
Z82206.1	chr22	39960397	39964718	+
PRKAB1	chr12	119667864	119681624	+
TMEM129	chr4	1715952	1721358	-
PIGL	chr17	16217191	16351797	+
ARAP1	chr11	72685069	72793599	-
MRPL30	chr2	99181152	99199561	+
ELP3	chr8	28089673	28191156	+
AC010422.3	chr19	12643831	12648397	-
EEF1G	chr11	62559596	62574086	-
SLC9A3	chr5	470456	524449	-
EIF2A	chr3	150546678	150586016	+
ARL6IP1	chr16	18791669	18801572	-
TMEM241	chr18	23197144	23437961	-
PKIG	chr20	44531785	44624247	+
ATF2	chr2	175072250	175168382	-
LENG8	chr19	54448887	54462037	+
TMEM248	chr7	66921225	66958551	+
FKBP4	chr12	2794970	2805423	+
TPT1	chr13	45333471	45341370	-
ELL	chr19	18442663	18522116	-
DPY19L1	chr7	34928876	35038271	-
CRYL1	chr13	20403666	20525873	-
RACK1	chr5	181236897	181248096	-

miRNA targets:

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC010442.1	chr5	466124	473098	-
AC104461.1	chr1	200333193	200478669	+
AL022311.1	chr22	37876148	37895563	+
AC116565.1	chr4	577168	618076	+
ESRG	chr3	54632122	54639857	-
MALAT1	chr11	65497688	65506516	+

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.