exRNAdisease

General Information

Database ID:

exR0010954

RNA Name:

PODXL

RNA Type:

mRNA

Chromosome:

chr7

Starnd:

Coordinate:

Start Site(bp):

131500262

End Site(bp):

131558217

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
AC004922.1	chr7	99325879	99394653	+
AC005943.1	chr19	1578339	1605445	-
AC010422.3	chr19	12643831	12648397	-
AC073508.2	chr17	40627356	40665141	-
AC091167.2	chr15	90249556	90272208	+
AC118553.2	chr1	99970011	100083321	+
AC135050.2	chr16	31083439	31094956	-
ACAA2	chr18	49782164	49813953	-
ACAD8	chr11	134253495	134265855	+
ACP1	chr2	264140	278283	+
ACTB	chr7	5527148	5563784	-
ACTG1	chr17	81509971	81523847	-
ACTR1A	chr10	102461881	102502712	-
ADCY3	chr2	24819169	24919839	-
ADD3	chr10	109996368	110135565	+
AFDN	chr6	167826922	167972023	+
AHCY	chr20	34280268	34311802	-
AIF1L	chr9	131096476	131123152	+
AKT1	chr14	104769349	104795751	-
AKT1S1	chr19	49869033	49878459	-
AL133352.1	chr10	100505628	100529881	-
AL162417.1	chr9	133098121	133163914	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-103a-3p	chr5	168560904	168560926	-
hsa-miR-4709-5p	chr14	74480175	74480196	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC016876.2	chr17	7581964	7584086	-

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.