exRNAdisease

General Information

Database ID:

exR0005618

RNA Name:

GDI2

RNA Type:

mRNA

Chromosome:

chr10

Starnd:

Coordinate:

Start Site(bp):

5765223

End Site(bp):

5842132

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
ADH5	chr4	99070978	99088801	-
ABHD17A	chr19	1876810	1885547	-
ADIPOR2	chr12	1688574	1788674	+
ACAA2	chr18	49782164	49813953	-
AC026954.2	chr17	7312661	7319174	-
AC010422.3	chr19	12643831	12648397	-
AC245033.1	chr15	82536788	82573194	-
AC008763.2	chr19	7629796	7643048	+
ADCY6	chr12	48766194	48789037	-
ADO	chr10	62804720	62808479	+
ACTB	chr7	5527148	5563784	-
ADK	chr10	74151202	74709963	+
AC073283.3	chr2	47065941	47176511	-
ACADVL	chr17	7217125	7225266	+
ALDOA	chr16	30064164	30070457	+
AD000671.1	chr19	35745678	35754519	+
ACADM	chr1	75724347	75787575	+
ADCY2	chr5	7396138	7830081	+
ADAMTS19	chr5	129460281	129738683	+
ADAMTS13	chr9	133414358	133459402	+
ACTG1	chr17	81509971	81523847	-
ACSL3	chr2	222860942	222944639	+
AC073508.2	chr17	40627356	40665141	-
AFDN	chr6	167826922	167972023	+
AFG3L2	chr18	12328944	12377227	-
ACOT9	chrX	23701055	23766475	-
ALDH18A1	chr10	95605941	95656711	-
AC000093.1	chr22	19717220	19724772	+
ACSS2	chr20	34872146	34927962	+
ABHD17B	chr9	71862452	71910931	-

miRNA targets:

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC009446.1	chr8	71675300	71702786	+
AC010542.4	chr16	66549280	66551189	+
AC016876.2	chr17	7581964	7584086	-
AC124068.2	chr15	89335053	89336161	+
AC147067.1	chr4	1574062	1580253	-
AC245033.4	chr15	82533175	82540008	-
AL021707.2	chr22	38667585	38681847	-

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.