exRNAdisease

General Information

Database ID:

exR0000399

RNA Name:

AHCYL1

RNA Type:

mRNA

Chromosome:

chr1

Starnd:

Coordinate:

Start Site(bp):

109984765

End Site(bp):

110023742

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
HDGF	chr1	156742109	156766925	-
PAK2	chr3	196739857	196832647	+
DCUN1D4	chr4	51843000	51916837	+
NUFIP2	chr17	29255839	29294148	-
ATP5MF	chr7	99448475	99466331	-
NACA	chr12	56712427	56731628	-
RPLP0	chr12	120196699	120201235	-
NECAB3	chr20	33657087	33674463	-
TPT1	chr13	45333471	45341370	-
INTS10	chr8	19817391	19852083	+
RPS12	chr6	132814569	132817564	+
RRM2B	chr8	102204502	102238961	-
ERP44	chr9	99979185	100099000	-
UBXN6	chr19	4444999	4457794	-
TUBA1B	chr12	49127782	49131397	-
ATP5PO	chr21	33903453	33915814	-
HSP90AB1	chr6	44246166	44253888	+
IMMT	chr2	86143932	86195770	-
TKT	chr3	53224712	53256052	-
MT-ND4	chrMT	10760	12137	+
HLA-DRB1	chr6	32578769	32589848	-
AL136454.1	chr1	192716132	192716653	+
SYNCRIP	chr6	85607785	85643792	-
SLC1A5	chr19	46774883	46788594	-
NRM	chr6	30688047	30691420	-
OPA3	chr19	45527427	45602212	-
PABPN1	chr14	23321289	23326185	+
DDIT4	chr10	72273924	72276036	+
RPS10-NUDT3	chr6	34284887	34426071	-
IDH1	chr2	208236227	208266074	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-574-5p	chr4	38868056	38868078	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC073529.1	chrX	10847578	11111220	-
AC092490.1	chr12	8788253	8795789	+
AD000090.1	chr19	35557956	35581954	+
AL022311.1	chr22	37876148	37895563	+
AC079354.2	chr2	202178660	202179391	-
LINC02190	chr16	31542748	31553604	-

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.