exRNAdisease

General Information

Database ID:

exR0010493

RNA Name:

PEBP1

RNA Type:

mRNA

Chromosome:

chr12

Starnd:

Coordinate:

Start Site(bp):

118136124

End Site(bp):

118145584

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
ABRACL	chr6	139028745	139043302	+
AC005258.1	chr19	2269525	2341172	+
AC008982.1	chr19	38817471	38840178	-
AC010422.3	chr19	12643831	12648397	-
AC091167.2	chr15	90249556	90272208	+
AC092143.1	chr16	89919165	89936092	+
AC139530.2	chr17	81703371	81720539	+
AC245033.1	chr15	82536788	82573194	-
ACAD9	chr3	128879596	128916067	+
ACTB	chr7	5527148	5563784	-
ADAM10	chr15	58588809	58749791	-
ADGRG2	chrX	18989307	19122637	-
ADNP2	chr18	80109262	80147523	+
ADSL	chr22	40346500	40390463	+
AEN	chr15	88621337	88632281	+
AKAP8L	chr19	15380050	15419141	-
AKR1B1	chr7	134442356	134459284	-
AL133352.1	chr10	100505628	100529881	-

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
AC023509.1	chr12	53441741	53467528	+
AC040162.3	chr16	67882461	67886367	+
AC068473.5	chr18	79677287	79679358	-
AC091564.7	chr11	6610883	6616594	-
AC132217.1	chr11	2129121	2129964	-
AC245033.4	chr15	82533175	82540008	-

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.