exRNAdisease

General Information

Database ID:

exR0000012

RNA Name:

AAGAB

RNA Type:

mRNA

Chromosome:

chr15

Starnd:

Coordinate:

Start Site(bp):

67200667

End Site(bp):

67255195

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
BTBD1	chr15	83016423	83067252	-
PIMREG	chr17	6444441	6451469	+
HNRNPA1	chr12	54280193	54287088	+
SETD1A	chr16	30957754	30984664	+
RAC3	chr17	82031678	82034204	+
ARF4	chr3	57571363	57598220	-
RPL27	chr17	42998273	43002959	+
HSDL1	chr16	84122141	84145192	-
CHD7	chr8	60678740	60868028	+
CRABP2	chr1	156699606	156705816	-
DUT	chr15	48331011	48343373	+
UNC119B	chr12	120710458	120723640	+
PRDM2	chr1	13700198	13825079	+
BCAP31	chrX	153700492	153724565	-
TOMM20	chr1	235109341	235128837	-
CDPF1	chr22	46244011	46250311	-
MRPL45	chr17	38297023	38323217	+
CHMP3	chr2	86503430	86563479	-
RPS23	chr5	82273320	82278396	-
RTN4	chr2	54972187	55112621	-
CCND2	chr12	4273762	4305353	+
FUS	chr16	31180110	31194871	+
YWHAQ	chr2	9583967	9630997	-
PFN1	chr17	4945652	4949061	-
GPAM	chr10	112149865	112215377	-
HYAL2	chr3	50317790	50322782	-
R3HDM1	chr2	135531455	135725270	+
FTL	chr19	48965309	48966879	+
RPL10A	chr6	35468401	35470785	+
RIC1	chr9	5629025	5776557	+

miRNA targets:

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
HLA-F-AS1	chr6	29726601	29749049	-
PARD6G-AS1	chr18	80147924	80179839	+

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.