exRNAdisease

General Information

Database ID:

exR0000435

RNA Name:

AKAP1

RNA Type:

mRNA

Chromosome:

chr17

Starnd:

Coordinate:

Start Site(bp):

57085092

End Site(bp):

57121346

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
LRCH3	chr3	197791226	197888436	+
TP53I11	chr11	44885903	44951306	-
UNKL	chr16	1363205	1414751	-
NUP210	chr3	13316235	13420322	-
CUEDC2	chr10	102423245	102432584	-
TAF6	chr7	100107070	100119841	-
MT-ND4	chrMT	10760	12137	+
YME1L1	chr10	27110112	27155266	-
NOP56	chr20	2652593	2658393	+
TAOK2	chr16	29973868	29992261	+
LIN28A	chr1	26410817	26429728	+
TBC1D9B	chr5	179862066	179907859	-
PLCG2	chr16	81739097	81962685	+
CYBRD1	chr2	171522247	171558129	+
ABCE1	chr4	145098288	145129524	+
NAP1L4	chr11	2944431	2992377	-
CC2D1B	chr1	52345723	52366193	-
WASF2	chr1	27404230	27490167	-
TMEM41A	chr3	185476496	185499057	-
NAPA	chr19	47487637	47515091	-
TPRG1L	chr1	3625015	3630127	+
TOP2A	chr17	40388525	40417896	-
RAN	chr12	130872037	130877678	+
SENP3-EIF4A1	chr17	7563287	7578715	+
TSC22D1	chr13	44432143	44577147	-
SLC2A11	chr22	23856703	23886309	+
FKRP	chr19	46746046	46776988	+
UBL5	chr19	9827892	9830115	+
LMAN2	chr5	177331567	177351668	-
POLL	chr10	101578882	101588270	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-1197	chr14	101025620	101025640	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC005618.1	chr5	141326210	141329357	+
AC016876.2	chr17	7581964	7584086	-
AC008738.1	chr19	33178056	33178651	+
ERVK13-1	chr16	2660348	2682379	-
LINC00458	chr13	54115783	54142319	-
XIST	chrX	73820649	73852723	-

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.