exRNAdisease

General Information

Database ID:

exR0000469

RNA Name:

AKT3

RNA Type:

mRNA

Chromosome:

chr1

Starnd:

Coordinate:

Start Site(bp):

243488233

End Site(bp):

243851079

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
NUP107	chr12	68686951	68745809	+
FUCA1	chr1	23845077	23868294	-
HNRNPK	chr9	83968083	83980616	-
RPL37	chr5	40825262	40835222	-
EDEM2	chr20	35115364	35147336	-
PRDX6	chr1	173477330	173488815	+
HLA-C	chr6	31268749	31272130	-
MAP3K7	chr6	90513573	90587072	-
SRSF4	chr1	29147743	29181900	-
IPMK	chr10	58191517	58267894	-
POLR2F	chr22	37952607	38041915	+
IST1	chr16	71845996	71931199	+
ID1	chr20	31605283	31606515	+
L1TD1	chr1	62194849	62212328	+
SF3B1	chr2	197388515	197435091	-
SDCCAG8	chr1	243256034	243500091	+
POLR1D	chr13	27620742	27744237	+
ESRP1	chr8	94641074	94707466	+
LAPTM4B	chr8	97775057	97853013	+
AKT2	chr19	40230317	40285536	-
STK4	chr20	44966479	45080021	+
HNRNPL	chr19	38836388	38852347	-
PAPOLA	chr14	96501433	96567111	+
PKN1	chr19	14433053	14471867	+
IL6R	chr1	154405193	154469450	+
TIMM10B	chr11	6481501	6484681	+
RPL13A	chr19	49487554	49492308	+
RTN4R	chr22	20241415	20283246	-
ANKFY1	chr17	4163821	4263995	-
SGSH	chr17	80206716	80220923	-

miRNA targets:

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
RMRP	chr9	35657751	35658018	-
SNHG1	chr11	62851984	62855953	-

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.