exRNAdisease

General Information

Database ID:

exR0000439

RNA Name:

AKAP13

RNA Type:

mRNA

Chromosome:

chr15

Starnd:

Coordinate:

Start Site(bp):

85380571

End Site(bp):

85749358

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
ZFAND6	chr15	80059568	80138393	+
FNBP1	chr9	129887187	130043194	-
IPO13	chr1	43946950	43968022	+
NUDT3	chr6	34279679	34392669	-
CXXC4	chr4	104468308	104494901	-
RPS4X	chrX	72255679	72277248	-
OSTF1	chr9	75088514	75147265	+
CLEC16A	chr16	10944564	11182186	+
HPS3	chr3	149129638	149173732	+
GCSAM	chr3	112120839	112133270	-
CAPN1	chr11	65180566	65212006	+
RBM3	chrX	48574449	48581162	+
GOLGA8B	chr15	34525207	34588503	-
HAUS5	chr19	35612735	35625355	+
CENPA	chr2	26764289	26801067	+
CTDNEP1	chr17	7243591	7252491	-
RBM47	chr4	40423267	40630875	-
PTEN	chr10	87863625	87971930	+
ZNF277	chr7	112206695	112343934	+
SLC17A9	chr20	62952707	62969585	+
SNTB2	chr16	69187129	69309052	+
CGGBP1	chr3	88051944	88149885	-
ARIH1	chr15	72474330	72602987	+
ST6GALNAC6	chr9	127885321	127905408	-
ATP5PF	chr21	25716503	25735673	-
PSMG1	chr21	39174769	39183488	-
PCYT2	chr17	81900965	81911464	-
CHD3	chr17	7884796	7912760	+
ZNF354B	chr5	178859953	178888122	+
TMCC2	chr1	205227946	205285632	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-449a	chr5	55170586	55170607	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC011603.2	chr12	49090208	49093312	+
AC016590.2	chr19	37337236	37337743	+
AC245014.3	chr1	145281116	145281462	+
AD000090.1	chr19	35557956	35581954	+
AL157935.2	chr9	127934503	127940952	+
AL355075.4	chr14	20343048	20343685	-
LINC01783	chr1	16533886	16536172	-
LINC02249	chr15	30195809	30217552	+
TMEM99	chr17	40819106	40836270	+

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.