exRNAdisease

General Information

Database ID:

exR0012322

RNA Name:

RPL13

RNA Type:

mRNA

Chromosome:

chr16

Starnd:

Coordinate:

Start Site(bp):

89560657

End Site(bp):

89566828

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
AGFG2	chr7	100539203	100568220	+
AC009690.1	chr15	72284727	72375981	-
ADO	chr10	62804720	62808479	+
AC008763.2	chr19	7629796	7643048	+
ALDH5A1	chr6	24494867	24537207	+
AK4	chr1	65147549	65232145	+
AGAP1	chr2	235494043	236131800	+
AAAS	chr12	53307456	53324864	-
AL136454.1	chr1	192716132	192716653	+
AL590132.1	chr1	210858125	211134146	-
ACTB	chr7	5527148	5563784	-
AC011455.2	chr19	38915404	38949855	-
ACAT2	chr6	159762045	159779112	+
ABCD3	chr1	94418389	94518666	+
AHCYL1	chr1	109984765	110023742	+
AK2	chr1	33007940	33080996	-
ACP1	chr2	264140	278283	+
AC004922.1	chr7	99325879	99394653	+
ADPRHL2	chr1	36088892	36093932	+
AARS2	chr6	44298731	44313347	-
AC006030.1	chr2	74211604	74363377	-
AIFM2	chr10	70098223	70132934	-
ACADM	chr1	75724347	75787575	+
AC026464.4	chr16	69299682	69322700	+
ADCY3	chr2	24819169	24919839	-
ACTR3	chr2	113890063	113962596	+
ADPGK	chr15	72751369	72785846	-
ACOT7	chr1	6264269	6394391	-
AKIRIN1	chr1	38991276	39006059	+
ALDH2	chr12	111766887	111817532	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-29c-3p	chr1	207801865	207801886	-
hsa-miR-4426	chr1	192716333	192716349	+
hsa-miR-4485-3p	chr11	10508277	10508296	-
hsa-miR-4521	chr17	8186948	8186969	+
hsa-miR-6716-3p	chr11	118644048	118644069	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC002116.1	chr19	36008638	36014235	-
AC007952.4	chr17	19112000	19112636	-
AC009022.1	chr16	69976297	70065948	-
AC010542.4	chr16	66549280	66551189	+
AC011632.1	chr8	74798784	74866939	-
AC016747.1	chr2	61141592	61144969	-
AC020928.2	chr19	36773712	36775908	-
AC026362.1	chr12	122975320	122982907	+
AC026401.3	chr16	15701237	15702118	+
AC068768.1	chr12	123262060	123262402	+
AC091564.7	chr11	6610883	6616594	-
AC092143.3	chr16	89906157	89918233	+
AC100810.1	chr8	1761054	1764508	-
AC132217.1	chr11	2129121	2129964	-
AC133644.3	chr2	87455476	87767359	+
AC139149.1	chr17	81514047	81527776	+
AC215522.2	chr7	19018	35489	-
AC245014.3	chr1	145281116	145281462	+
AC245033.4	chr15	82533175	82540008	-
AD000090.1	chr19	35557956	35581954	+
AF106564.1	chr8	24912165	24914717	-
AL022311.1	chr22	37876148	37895563	+
AL022341.1	chr16	648473	649200	-

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.