exRNAdisease

General Information

Database ID:

exR0000394

RNA Name:

AGTRAP

RNA Type:

mRNA

Chromosome:

chr1

Starnd:

Coordinate:

Start Site(bp):

11736084

End Site(bp):

11754802

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
LDHA	chr11	18394560	18408425	+
STK4	chr20	44966479	45080021	+
ACPP	chr3	132317369	132368298	+
HOXB1	chr17	48528526	48531011	-
TMSB4X	chrX	12975110	12977227	+
PAFAH1B3	chr19	42297033	42303546	-
KDM3A	chr2	86440647	86492716	+
ICE1	chr5	5420664	5490220	+
CCDC88C	chr14	91271323	91417844	-
TUBA1C	chr12	49188736	49274603	+
POGK	chr1	166839447	166856344	+
NUCB1	chr19	48900312	48923372	+
RPL30	chr8	98024851	98046469	-
HSF1	chr8	144291591	144314720	+
PABPC3	chr13	25095868	25099254	+
PABPN1	chr14	23321289	23326185	+
KRT19	chr17	41523617	41528308	-
SLC2A13	chr12	39755025	40106089	-
UBE2T	chr1	202331657	202341980	-
XPC	chr3	14145147	14178783	-
FUS	chr16	31180110	31194871	+
TJAP1	chr6	43477523	43506556	+
MAD2L2	chr1	11674480	11691650	-
CNPY3	chr6	42929192	42939294	+
STAT5B	chr17	42199177	42276707	-
SCARB1	chr12	124776856	124882668	-
IQGAP1	chr15	90388242	90502239	+
SND1	chr7	127652194	128092609	+
HLA-B	chr6	31269491	31357188	-
APEH	chr3	49674014	49683971	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-34a-5p	chr1	9151735	9151756	-
hsa-miR-188-5p	chrX	50003517	50003537	+
hsa-miR-34c-5p	chr11	111513451	111513473	+
hsa-miR-324-5p	chr17	7223343	7223364	-
hsa-miR-654-5p	chr14	101040234	101040255	+
hsa-miR-129-2-3p	chr11	43581450	43581471	+
hsa-miR-330-5p	chr19	45639049	45639070	-
hsa-miR-628-5p	chr15	55372991	55373012	-
hsa-miR-541-3p	chr14	101064548	101064569	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AD000090.1	chr19	35557956	35581954	+
MIR663AHG	chr20	26167817	26251546	-

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.