exRNAdisease

General Information

Database ID:

exR0000021

RNA Name:

AASDHPPT

RNA Type:

mRNA

Chromosome:

chr11

Starnd:

Coordinate:

Start Site(bp):

106075501

End Site(bp):

106098699

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
GTF2F2	chr13	45120510	45284893	+
CFL1	chr11	65823022	65862026	-
NUP93	chr16	56730118	56850286	+
HSD17B8	chr6	33204655	33206831	+
RPL3	chr22	39312882	39320389	-
RASSF3	chr12	64507001	64697564	+
TMBIM6	chr12	49707725	49764934	+
HNRNPL	chr19	38836388	38852347	-
CXXC4	chr4	104468308	104494901	-
PSME3	chr17	42824385	42843760	+
AHCY	chr20	34280268	34311802	-
ESRP1	chr8	94641074	94707466	+
AKAP10	chr17	19904302	19978343	-
PCLAF	chr15	64364304	64387687	-
COA3	chr17	42795147	42798704	-
MTA2	chr11	62593214	62601865	-
EIF4G2	chr11	10797050	10808940	-
WDR73	chr15	84639281	84654343	-
PUM2	chr2	20248691	20352234	-
GTPBP6	chrX	304529	318819	-
NAP1L4	chr11	2944431	2992377	-
MATR3	chr5	139273752	139331671	+
IRF7	chr11	612553	615983	-
SINHCAF	chr12	31280584	31327058	-
RAB8A	chr19	16111889	16134234	+
SPG21	chr15	64963022	64990310	-
PANK3	chr5	168548495	168579368	-
DIAPH1	chr5	141515016	141619055	-
RPS29	chr14	49570984	49599164	-
HMGA1	chr6	34236873	34246231	+

miRNA targets:

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC064807.1	chr8	51899268	51949874	+

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.