exRNAdisease

General Information

Database ID:

exR0003763

RNA Name:

DDX5

RNA Type:

mRNA

Chromosome:

chr17

Starnd:

Coordinate:

Start Site(bp):

64498254

End Site(bp):

64508199

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
ABCB4	chr7	87401697	87480435	-
ABCB7	chrX	75051048	75156732	-
ABCF2	chr7	151207837	151227166	-
AC005258.1	chr19	2269525	2341172	+
AC010132.3	chr7	42909273	42932174	-
AC010422.3	chr19	12643831	12648397	-
AC024592.3	chr19	5866171	5903787	-
AC048338.1	chr12	122207779	122266423	-
AC093525.2	chr16	2496032	2520218	+
AC120057.2	chr17	7240427	7244635	-
AC245033.1	chr15	82536788	82573194	-
ACOT13	chr6	24667035	24705065	+
ACSS2	chr20	34872146	34927962	+
ADA2	chr22	17178790	17258235	-
ADIPOR2	chr12	1688574	1788674	+
AFDN	chr6	167826922	167972023	+
AGFG2	chr7	100539203	100568220	+
AGO1	chr1	35869808	35930532	+
AGO4	chr1	35808016	35857890	+
AGPAT5	chr8	6708642	6761503	+
AHDC1	chr1	27534035	27604431	-
AKAP12	chr6	151239967	151358559	+
AKIRIN1	chr1	38991276	39006059	+
AL133352.1	chr10	100505628	100529881	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-18a-5p	chr13	91350756	91350778	+
hsa-miR-33a-5p	chr22	41900949	41900969	+
hsa-miR-141-3p	chr12	6964155	6964176	+
hsa-miR-206	chr6	52144401	52144422	+
hsa-miR-302b-3p	chr4	112648489	112648511	-
hsa-miR-33b-5p	chr17	17813897	17813916	-
hsa-miR-3064-5p	chr17	64500817	64500837	-
hsa-miR-3064-3p	chr17	64500775	64500797	-
hsa-miR-5047	chr17	64501230	64501250	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC020663.1	chr16	4730115	4752565	-
AC023509.1	chr12	53441741	53467528	+
AC079781.5	chr7	97851688	97972985	-

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.