exRNAdisease

General Information

Database ID:

exR0000438

RNA Name:

AKAP12

RNA Type:

mRNA

Chromosome:

chr6

Starnd:

Coordinate:

Start Site(bp):

151239967

End Site(bp):

151358559

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
MAVS	chr20	3846799	3876123	+
CALM1	chr14	90396502	90408268	+
AP1B1	chr22	29327680	29423179	-
SLC25A3	chr12	98593591	98606379	+
MEPCE	chr7	100428790	100434118	+
PLCXD1	chrX	276322	303356	+
CEP68	chr2	65056366	65087004	+
ARNT	chr1	150809713	150876708	-
SLC3A2	chr11	62856102	62888875	+
PAQR3	chr4	78887127	78939438	-
RAB3GAP1	chr2	135052265	135176394	+
ACTG1	chr17	81509971	81523847	-
TMBIM6	chr12	49707725	49764934	+
ZNF646	chr16	31074422	31084196	+
PSME4	chr2	53864069	53970993	-
TAF10	chr11	6606294	6612539	-
LAMP1	chr13	113297239	113323672	+
HNRNPF	chr10	43385617	43409166	-
ADGRG6	chr6	142301854	142446266	+
SNX3	chr6	108211222	108261246	-
GPHN	chr14	66507407	67181803	+
PARN	chr16	14435700	14632728	-
UNC45A	chr15	90930180	90954093	+
HERC2	chr15	28111040	28322172	-
B4GALT4	chr3	119211732	119240946	-
DSTN	chr20	17570075	17609919	+
ADGRL1	chr19	14147743	14206187	-
MTHFD2	chr2	74198610	74217565	+
SC5D	chr11	121292681	121313410	+
STT3B	chr3	31532638	31637616	+

miRNA targets:

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC091564.7	chr11	6610883	6616594	-

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.