exRNAdisease

General Information

Database ID:

exR0000219

RNA Name:

ACY1

RNA Type:

mRNA

Chromosome:

chr3

Starnd:

Coordinate:

Start Site(bp):

51983340

End Site(bp):

51989197

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
INVS	chr9	100099243	100302175	+
PPP2R5E	chr14	63371364	63543377	-
SRSF1	chr17	58000919	58007346	-
ANP32A	chr15	68778535	68820897	-
KDELR2	chr7	6445953	6484190	-
OAS2	chr12	112978395	113011723	+
ILF3	chr19	10654261	10692417	+
SLC25A3	chr12	98593591	98606379	+
ABCG2	chr4	88090150	88231628	-
MAPK3	chr16	30114105	30123506	-
TUBA1B	chr12	49127782	49131397	-
NEDD8	chr14	24216857	24232367	-
ABHD14A-ACY1	chr3	51974706	51989183	+
LASP1	chr17	38869859	38921770	+
HERC1	chr15	63608618	63833948	-
LRIG3	chr12	58872149	58920522	-
TPI1	chr12	6867119	6870948	+
ZNF623	chr8	143636013	143656418	+
UBC	chr12	124911604	124917368	-
RPS3	chr11	75399515	75422280	+
RBM38	chr20	57391396	57409333	+
UCKL1	chr20	63939829	63956416	-
PPTC7	chr12	110533245	110583318	-
TRIM28	chr19	58544064	58550722	+
RPLP0	chr12	120196699	120201235	-
PABPN1	chr14	23321289	23326185	+
GANAB	chr11	62624826	62646726	-
PLAT	chr8	42174718	42207676	-
TMEM184B	chr22	38219291	38273010	-
GNL3	chr3	52681156	52694497	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-625-5p	chr14	65471116	65471136	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AD000090.1	chr19	35557956	35581954	+
DANCR	chr4	52712404	52720351	+

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.