exRNAdisease

General Information

Database ID:

exR0010592

RNA Name:

PHB2

RNA Type:

mRNA

Chromosome:

chr12

Starnd:

Coordinate:

Start Site(bp):

6965327

End Site(bp):

6970753

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	-
ABL1	chr9	130713016	130887675	+
ABT1	chr6	26596953	26600739	+
AC004832.3	chr22	30409255	30428990	+
AC006064.6	chr12	6556886	6607367	-
AC007192.1	chr19	18153158	18178117	+
AC010422.3	chr19	12643831	12648397	-
AC011511.1	chr19	10305427	10316009	-
AC093525.1	chr16	2513965	2527955	+
AC245033.1	chr15	82536788	82573194	-
ACAT1	chr11	108116695	108147603	+
ACIN1	chr14	23058564	23095614	-
ACTB	chr7	5527148	5563784	-
ACTG1	chr17	81509971	81523847	-
ACTN4	chr19	38647649	38731589	+
ADAR	chr1	154582057	154628013	-
ADCY1	chr7	45574140	45723116	+
ADCY2	chr5	7396138	7830081	+
ADCY3	chr2	24819169	24919839	-
ADD2	chr2	70607618	70768225	-
ADGRL2	chr1	81306160	81992436	+
ADNP2	chr18	80109262	80147523	+
AHRR	chr5	271670	438291	+
AL021546.1	chr12	120438198	120460006	+
ALAS1	chr3	52198086	52214327	+
ALDOA	chr16	30064164	30070457	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-491-5p	chr9	20716120	20716141	+
hsa-miR-625-5p	chr14	65471116	65471136	+
hsa-miR-744-5p	chr17	12081909	12081930	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC002116.1	chr19	36008638	36014235	-
AC006064.5	chr12	6510275	6510522	+
AC010642.2	chr19	58309727	58327248	-
AC016876.2	chr17	7581964	7584086	-
AC023509.1	chr12	53441741	53467528	+
AC091564.7	chr11	6610883	6616594	-
AC139149.1	chr17	81514047	81527776	+
AC245033.4	chr15	82533175	82540008	-
AD000090.1	chr19	35557956	35581954	+

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.