exRNAdisease

General Information

Database ID:

exR0000318

RNA Name:

ADNP2

RNA Type:

mRNA

Chromosome:

chr18

Starnd:

Coordinate:

Start Site(bp):

80109262

End Site(bp):

80147523

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
PWP2	chr21	44107373	44131181	+
USP14	chr18	158383	214629	+
ERBB2	chr17	39687914	39730426	+
EEF2	chr19	3976056	3985463	-
MT-ND2	chrMT	4470	5511	+
RPL26	chr17	8377516	8383213	-
TOM1L2	chr17	17843511	17972422	-
DSC2	chr18	31058840	31102522	-
ARID4B	chr1	235131634	235328219	-
FBXO42	chr1	16246840	16352480	-
PEBP1	chr12	118136124	118145584	+
CDC42EP3	chr2	37641882	37738468	-
NOMO3	chr16	16232528	16294811	+
PTMA	chr2	231706895	231713541	+
ACTA2	chr10	88935074	88991339	-
ACTB	chr7	5527148	5563784	-
PRKCI	chr3	170222424	170305977	+
TOMM70	chr3	100363431	100401089	-
FP565260.1	chr21	5130871	5154658	-
RPS20	chr8	56067295	56074581	-
SH3GLB1	chr1	86704570	86748184	+
GRID2IP	chr7	6497462	6551436	-
COL4A2	chr13	110305812	110513209	+
PGP	chr16	2211593	2214840	-
CERS6	chr2	168455862	168775137	+
NAP1L1	chr12	76036585	76084958	-
ALDOA	chr16	30064164	30070457	+
RPA2	chr1	27891524	27914746	-
ITM2C	chr2	230864639	230879248	+
CALR	chr19	12938578	12944489	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-4508	chr15	23562107	23562123	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC007218.1	chr16	9666885	9676843	-
AC135178.2	chr17	8318088	8318712	-
AL391294.1	chrX	81000150	81004217	-
HOXA-AS2	chr7	27107777	27134302	+

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.