exRNAdisease

General Information

Database ID:

exR0000427

RNA Name:

AK2

RNA Type:

mRNA

Chromosome:

chr1

Starnd:

Coordinate:

Start Site(bp):

33007940

End Site(bp):

33080996

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
IFI30	chr19	18173162	18178117	+
C19orf53	chr19	13774456	13778773	+
RBM10	chrX	47145221	47186813	+
RPL5	chr1	92832013	92841924	+
SAP30BP	chr17	75667251	75708062	+
PPP2CA	chr5	134194332	134226073	-
RPLP1	chr15	69452814	69456205	+
REXO1	chr19	1815248	1848483	-
ARL2BP	chr16	57245259	57253635	+
GTF3C5	chr9	133030675	133058503	+
GRID1	chr10	85599552	86366795	-
OGFOD3	chr17	82389210	82418637	-
MRPL4	chr19	10251901	10260055	+
EIF4E	chr4	98871684	98930637	-
DDIT4	chr10	72273924	72276036	+
MYBBP1A	chr17	4538897	4555631	-
MZT1	chr13	72708367	72727629	-
AC011448.1	chr19	19516227	19536076	+
MTRNR2L1	chr17	22523111	22524663	+
CDC42SE1	chr1	151050971	151070325	-
HAUS1	chr18	46104378	46128333	+
POMP	chr13	28659104	28678959	+
AP2A1	chr19	49766968	49807113	+
HLA-B	chr6	31269491	31357188	-
OCIAD1	chr4	48805212	48861817	+
MAL2	chr8	119165034	119245673	+
RPS5	chr19	58386400	58394806	+
HLA-DQB1	chr6	32659467	32668383	-
STRAP	chr12	15882387	15903478	+
SLC25A37	chr8	23528956	23575463	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-204-5p	chr9	70810031	70810052	-
hsa-miR-211-5p	chr15	31065095	31065116	-
hsa-miR-141-3p	chr12	6964155	6964176	+
hsa-miR-299-3p	chr14	101023832	101023853	+
hsa-miR-1224-5p	chr3	184241405	184241423	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC009133.5	chr16	29808679	29812227	+
AL121985.1	chr1	160670778	160699761	+
GUSBP11	chr22	23638487	23717356	-
LINC02381	chr12	54126082	54147485	+
LINC02539	chr6	137730170	137792835	-
MALAT1	chr11	65497688	65506516	+
SNHG17	chr20	38419638	38435409	-
SNHG5	chr6	85650491	85678932	-

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.