exRNAdisease

General Information

Database ID:

exR0015675

RNA Name:

UBC

RNA Type:

mRNA

Chromosome:

chr12

Starnd:

Coordinate:

Start Site(bp):

124911604

End Site(bp):

124917368

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
ABCF2	chr7	151207837	151227166	-
AC008982.1	chr19	38817471	38840178	-
AC018523.2	chr11	14493783	14520344	-
AC026954.2	chr17	7312661	7319174	-
AC118553.2	chr1	99970011	100083321	+
AC124312.1	chr15	24955034	25000276	+
AC138811.2	chr16	18788063	18801519	-
ACADVL	chr17	7217125	7225266	+
ACOT2	chr14	73567620	73575658	+
ACP5	chr19	11574660	11579008	-
ACTB	chr7	5527148	5563784	-
ACTG1	chr17	81509971	81523847	-
ACY1	chr3	51983340	51989197	+
ADAM10	chr15	58588809	58749791	-
ADIPOR2	chr12	1688574	1788674	+
AEN	chr15	88621337	88632281	+
AFF1	chr4	86935002	87141054	+
AFP	chr4	73431138	73456174	+
AGPAT1	chr6	32168212	32178096	-
AKIRIN2	chr6	87674860	87702233	-
AL133352.1	chr10	100505628	100529881	-
AL136295.1	chr14	24189157	24213473	-
AL136295.4	chr14	24180395	24190416	-
AL136454.1	chr1	192716132	192716653	+
ALDOA	chr16	30064164	30070457	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-492	chr12	94834427	94834449	+
hsa-miR-1244	chr2	231713368	231713393	+
hsa-miR-4426	chr1	192716333	192716349	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC048341.1	chr12	62602752	62622213	+
AC069281.2	chr7	100572232	100578700	-
AC091564.7	chr11	6610883	6616594	-
AC139149.1	chr17	81514047	81527776	+
AL022311.1	chr22	37876148	37895563	+
AL117378.1	chr6	131901963	131920565	+

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.