exRNAdisease

General Information

Database ID:

exR0003740

RNA Name:

DDX17

RNA Type:

mRNA

Chromosome:

chr22

Starnd:

Coordinate:

Start Site(bp):

38483438

End Site(bp):

38507660

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
AAMP	chr2	218264123	218270257	-
AAR2	chr20	36236459	36270918	+
AATF	chr17	36948954	37056871	+
ABHD8	chr19	17292131	17310236	-
AC005258.1	chr19	2269525	2341172	+
AC006064.6	chr12	6556886	6607367	-
AC007998.2	chr18	35443871	35497940	-
AC015813.2	chr17	57989038	58007246	-
AC107871.1	chr15	68184032	68229718	-
AC120057.2	chr17	7240427	7244635	-
ACIN1	chr14	23058564	23095614	-
ACTB	chr7	5527148	5563784	-
ACTN1	chr14	68874143	68979440	-
ACVR2A	chr2	147844517	147930826	+
ACVR2B	chr3	38453890	38493142	+
ADAM10	chr15	58588809	58749791	-
ADAM19	chr5	157395534	157575775	-
ADAR	chr1	154582057	154628013	-
ADD1	chr4	2843857	2930076	+
AEN	chr15	88621337	88632281	+
AHCY	chr20	34280268	34311802	-
AKT2	chr19	40230317	40285536	-
AL133352.1	chr10	100505628	100529881	-
AL136295.5	chr14	24147548	24166452	+
AL136454.1	chr1	192716132	192716653	+
AL358113.1	chr9	69035747	69255187	+
AL928654.3	chr14	105487199	105492267	+
ALDH16A1	chr19	49453225	49471050	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-302d-3p	chr4	112648006	112648028	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC007952.4	chr17	19112000	19112636	-
AC007998.3	chr18	35443869	35467088	-
AC016876.2	chr17	7581964	7584086	-
AC018809.2	chr3	9958717	9962539	+
AC067852.1	chr17	42536510	42562062	+
AC132217.1	chr11	2129121	2129964	-
AC245014.3	chr1	145281116	145281462	+
AD000090.1	chr19	35557956	35581954	+
AL132780.1	chr14	22929607	22956374	+

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.