exRNAdisease

General Information

Database ID:

exR0000406

RNA Name:

AHRR

RNA Type:

mRNA

Chromosome:

chr5

Starnd:

Coordinate:

Start Site(bp):

271670

End Site(bp):

438291

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
ALDOA	chr16	30064164	30070457	+
CARM1	chr19	10871513	10923070	+
COQ2	chr4	83261536	83284914	-
DDA1	chr19	17309518	17323298	+
GATAD1	chr7	92447482	92460075	+
GATM	chr15	45361124	45402327	-
HLA-C	chr6	31268749	31272130	-
HLA-DQA1	chr6	32628179	32647062	+
KIF2C	chr1	44739818	44767767	+
LPGAT1	chr1	211743457	211830763	-
MTMR3	chr22	29883155	30030866	+
NAMPT	chr7	106248298	106286326	-
NDUFS7	chr19	1383527	1395589	+
PDCD6	chr5	271621	314974	+
PHB2	chr12	6965327	6970753	-
PRKRIP1	chr7	102363872	102426676	+
PUS7	chr7	105439661	105522271	-
RPL11	chr1	23691742	23696835	+
RPL13	chr16	89560657	89566828	+
RPS19	chr19	41860255	41872925	+
RPS8	chr1	44775251	44778779	+
SDHA	chr5	218241	257082	+
STRAP	chr12	15882387	15903478	+
TAF1C	chr16	84177847	84187070	-
THAP7	chr22	20999104	21002196	-
TRAPPC6A	chr19	45162928	45178237	-
TRIM65	chr17	75880335	75896951	-
YIF1A	chr11	66284580	66289145	-
ZNF764	chr16	30553764	30558498	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-155-5p	chr21	25573983	25574006	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
MIR155HG	chr21	25561909	25575168	+

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.