exRNAdisease

General Information

Database ID:

exR0000095

RNA Name:

ABL1

RNA Type:

mRNA

Chromosome:

chr9

Starnd:

Coordinate:

Start Site(bp):

130713016

End Site(bp):

130887675

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
CXCL12	chr10	44370165	44386493	-
ASXL2	chr2	25733753	25878487	-
TMEM115	chr3	50354750	50359521	-
STK11	chr19	1177558	1228431	+
TMEM214	chr2	27032910	27041694	+
NOP53	chr19	47745546	47757058	+
TSC2	chr16	2047967	2089491	+
CHTOP	chr1	153633982	153646306	+
ZMYM3	chrX	71239624	71255146	-
NUTF2	chr16	67846923	67872567	+
DBNDD2	chr20	45406057	45410610	+
PCGF2	chr17	38733898	38749817	-
TM9SF3	chr10	96518110	96587452	-
CHD4	chr12	6570082	6614524	-
AP000350.4	chr22	23862188	23895223	+
PLCG1	chr20	41136960	41196801	+
ACTB	chr7	5527148	5563784	-
ATE1	chr10	121740421	121928801	-
TSPAN6	chrX	100627108	100639991	-
TRAF2	chr9	136881912	136926607	+
HMGN4	chr6	26538366	26546933	+
ETS2	chr21	38805183	38824955	+
LAMP5	chr20	9514358	9530524	+
MOV10	chr1	112673141	112700746	+
GLUL	chr1	182381704	182392206	-
TPM4	chr19	16067021	16103002	+
SIGIRR	chr11	405716	417455	-
HNRNPD	chr4	82352498	82374503	-
CORO7	chr16	4354542	4425705	-
ZNF319	chr16	57994668	58000453	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-432-5p	chr14	100884496	100884518	+
hsa-miR-520a-5p	chr19	53690895	53690915	+
hsa-miR-650	chr22	22822791	22822811	+
hsa-miR-330-5p	chr19	45639049	45639070	-
hsa-miR-760	chr1	93846880	93846899	+
hsa-miR-1270	chr19	20399320	20399342	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC007993.3	chr17	43914433	43923001	-
AC069281.2	chr7	100572232	100578700	-
NEAT1	chr11	65422774	65445540	+

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.