exRNAdisease

General Information

Database ID:

exR0000401

RNA Name:

AHDC1

RNA Type:

mRNA

Chromosome:

chr1

Starnd:

Coordinate:

Start Site(bp):

27534035

End Site(bp):

27604431

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
MTRNR2L10	chrX	55181392	55182442	-
EFNB2	chr13	106489745	106535662	-
DCUN1D4	chr4	51843000	51916837	+
PI4KA	chr22	20707691	20859417	-
PABPC1	chr8	100685816	100722809	-
PTBP1	chr19	797075	812327	+
TMEM107	chr17	8172457	8176399	-
ALDOA	chr16	30064164	30070457	+
ATRAID	chr2	27212027	27217178	+
LOXL3	chr2	74532258	74555690	-
FAM32A	chr19	16185380	16192046	+
EDARADD	chr1	236348257	236502915	+
EDC4	chr16	67873052	67884499	+
NUP188	chr9	128947699	129007096	+
ARHGAP33	chr19	35774532	35788822	+
SLC25A33	chr1	9539465	9585173	+
EP400	chr12	131949942	132080460	+
AIF1L	chr9	131096476	131123152	+
PRR14L	chr22	31676256	31750140	-
LPGAT1	chr1	211743457	211830763	-
RPS5	chr19	58386400	58394806	+
HCLS1	chr3	121631399	121660927	-
TOE1	chr1	45340052	45343973	+
CDK10	chr16	89680737	89696354	+
ATP1A1	chr1	116372668	116410261	+
NCBP1	chr9	97633668	97673748	+
CRTC1	chr19	18683678	18782333	+
WDR45B	chr17	82614562	82648553	-
GMEB2	chr20	63587602	63627101	-
RMI2	chr16	11249619	11381662	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-138-5p	chr16	56858527	56858549	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC138932.3	chr16	14909887	14911345	-

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.