exRNAdisease

General Information

Database ID:

exR0000073

RNA Name:

ABHD12

RNA Type:

mRNA

Chromosome:

chr20

Starnd:

Coordinate:

Start Site(bp):

25294742

End Site(bp):

25390835

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
NAT8L	chr4	2059327	2069089	+
MAN2A1	chr5	109689366	109869625	+
CUTC	chr10	99702558	99756134	+
ERAL1	chr17	28855010	28861061	+
HMOX1	chr22	35380361	35394207	+
MSL2	chr3	136148917	136197241	-
ERBB2	chr17	39687914	39730426	+
RPL8	chr8	144789765	144792587	-
MX1	chr21	41420304	41459214	+
ACP6	chr1	147629652	147670524	-
SIRT6	chr19	4174109	4182566	-
LSM7	chr19	2321520	2328611	-
PDCD2L	chr19	34404399	34426168	+
TPX2	chr20	31739271	31801805	+
ZNF764	chr16	30553764	30558498	-
TSPAN3	chr15	77041404	77083984	-
CXADR	chr21	17513043	17593579	+
ARIH2	chr3	48918821	48986382	+
RBM27	chr5	146203605	146289223	+
GINS1	chr20	25407673	25452628	+
UBE2J1	chr6	89326625	89352722	-
RBM22	chr5	150690792	150701077	-
EEF2	chr19	3976056	3985463	-
MED16	chr19	867630	893218	-
CYB5R3	chr22	42617840	42649392	-
PHIP	chr6	78934419	79078254	-
RBFA	chr18	80034389	80050651	+
EIF2S2	chr20	34088309	34112243	-
FKBP10	chr17	41812680	41823213	+
EML4	chr2	42169353	42332548	+

miRNA targets:

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC012236.1	chr15	31221999	31230838	-
AD000090.1	chr19	35557956	35581954	+
AL135925.1	chr10	79825902	79827602	+
SNHG22	chr18	49814023	49851059	+
XIST	chrX	73820649	73852723	-

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.