exRNAdisease

General Information

Database ID:

exR0000429

RNA Name:

AK4

RNA Type:

mRNA

Chromosome:

chr1

Starnd:

Coordinate:

Start Site(bp):

65147549

End Site(bp):

65232145

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
MYH9	chr22	36281277	36388067	-
MAPKAPK2	chr1	206684944	206734283	+
RER1	chr1	2391775	2405442	+
RELA	chr11	65653597	65663090	-
SFXN1	chr5	175477062	175529742	+
SMN2	chr5	70049612	70078522	+
TNIP1	chr5	151029945	151093577	-
TM9SF3	chr10	96518110	96587452	-
DPH2	chr1	43970000	43973369	+
STAT1	chr2	190908460	191020960	-
CD22	chr19	35319261	35347361	+
IGF2	chr11	2129112	2141238	-
MTRNR2L1	chr17	22523111	22524663	+
UBE3A	chr15	25333728	25439051	-
NFATC2IP	chr16	28950807	28967097	+
RPL14	chr3	40457292	40468587	+
SDCBP	chr8	58552924	58582859	+
DHX15	chr4	24517441	24584554	-
TFRC	chr3	196027183	196082096	-
PPP5D1	chr19	46480796	46601200	-
YWHAB	chr20	44885702	44908532	+
ACTG1	chr17	81509971	81523847	-
RBCK1	chr20	407498	430966	+
TMED5	chr1	93149742	93180516	-
CBX3	chr7	26201162	26213607	+
APOE	chr19	44905791	44909393	+
RPL15	chr3	23916545	23924374	+
HLA-B	chr6	31269491	31357188	-
PATZ1	chr22	31325804	31346346	-
CD47	chr3	108043091	108091862	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-362-3p	chrX	50009005	50009026	+
hsa-miR-556-3p	chr1	162342600	162342621	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AL359924.1	chr1	237862175	237928321	+
AL627309.5	chr1	141474	173862	-
BX284668.2	chr1	16870945	16883659	+
LINC01641	chr1	227393554	227431035	+

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.