exRNAdisease

General Information

Database ID:

exR0000087

RNA Name:

ABHD4

RNA Type:

mRNA

Chromosome:

chr14

Starnd:

Coordinate:

Start Site(bp):

22598237

End Site(bp):

22613215

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
FAM219A	chr9	34398184	34458570	-
RPL32	chr3	12834485	12841582	-
ZNF708	chr19	21291160	21329425	-
AP2A1	chr19	49766968	49807113	+
ARHGEF4	chr2	130836916	131047263	+
POLD4	chr11	67350772	67356972	-
PITPNC1	chr17	67377281	67697261	+
TUBA1A	chr12	49184795	49189080	-
TRIP6	chr7	100867387	100873454	+
AXIN1	chr16	287440	352723	-
HAT1	chr2	171922448	171983686	+
MYL12A	chr18	3247481	3256236	+
HNRNPA1	chr12	54280193	54287088	+
PSMB8	chr6	32840717	32844679	-
MT-CO1	chrMT	5904	7445	+
GAPDH	chr12	6534512	6538374	+
CNPPD1	chr2	219171897	219178106	-
DDX1	chr2	15591178	15631111	+
HNRNPK	chr9	83968083	83980616	-
OGT	chrX	71533104	71575892	+
PUM1	chr1	30931506	31065991	-
BTBD2	chr19	1985438	2034881	-
PSAP	chr10	71816298	71851325	-
EWSR1	chr22	29268009	29300525	+
EIF6	chr20	35278911	35284985	-
KDM5B	chr1	202724495	202808487	-
CBSL	chr21	6444869	6468040	-
AL121753.1	chr20	35267885	35280043	-
CCT8	chr21	29055805	29073797	-
TRPV3	chr17	3510502	3557995	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-31-5p	chr9	21512158	21512178	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AGAP1-IT1	chr2	235505751	235507566	+
GATA2-AS1	chr3	128489212	128502970	+

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.