exRNAdisease

General Information

Database ID:

exR0012387

RNA Name:

RPS11

RNA Type:

mRNA

Chromosome:

chr19

Starnd:

Coordinate:

Start Site(bp):

49496365

End Site(bp):

49499708

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
AC245033.1	chr15	82536788	82573194	-
ADCY1	chr7	45574140	45723116	+
ADAR	chr1	154582057	154628013	-
AK2	chr1	33007940	33080996	-
ADGRL1	chr19	14147743	14206187	-
ADH5	chr4	99070978	99088801	-
AC131160.1	chr3	183815568	183884889	-
AAGAB	chr15	67200667	67255195	-
ACTG1	chr17	81509971	81523847	-
AL138752.2	chr9	37588413	38068687	-
ABCE1	chr4	145098288	145129524	+
AIP	chr11	67483026	67491103	+
AC010422.3	chr19	12643831	12648397	-
AC099811.2	chr17	42119674	42154916	-
AC079594.2	chr3	160227454	160449829	-
AL603832.3	chr1	112702614	112711433	-
ABHD18	chr4	127965306	128039927	+
ADGRL2	chr1	81306160	81992436	+
AC138811.2	chr16	18788063	18801519	-
AKIRIN1	chr1	38991276	39006059	+
AL162231.3	chr9	34646645	34657113	+
ALDH18A1	chr10	95605941	95656711	-
AC004922.1	chr7	99325879	99394653	+
ACSS2	chr20	34872146	34927962	+
AC007192.1	chr19	18153158	18178117	+
AC005258.1	chr19	2269525	2341172	+
ADAM10	chr15	58588809	58749791	-
AFDN	chr6	167826922	167972023	+
AL133352.1	chr10	100505628	100529881	-
ALDOA	chr16	30064164	30070457	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-210-3p	chr11	568112	568133	-
hsa-miR-632	chr17	32350169	32350187	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC004687.1	chr17	58330884	58332508	-
AC010624.2	chr19	50075123	50075902	+
AC108134.2	chr16	3156736	3157483	-
AD000090.1	chr19	35557956	35581954	+
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.