exRNAdisease

General Information

Database ID:

exR0012401

RNA Name:

RPS23

RNA Type:

mRNA

Chromosome:

chr5

Starnd:

Coordinate:

Start Site(bp):

82273320

End Site(bp):

82278396

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
AKIRIN2	chr6	87674860	87702233	-
ABCA1	chr9	104781006	104928155	-
AC105052.1	chr7	102582523	102642869	-
AC137834.1	chr12	57249609	57296484	-
ALDOA	chr16	30064164	30070457	+
ACTN4	chr19	38647649	38731589	+
ACTR2	chr2	65227753	65271253	+
ADNP	chr20	50888916	50931437	-
ABL1	chr9	130713016	130887675	+
AL365205.1	chr6	41780349	41790141	+
AIP	chr11	67483026	67491103	+
AL133352.1	chr10	100505628	100529881	-
ACOT7	chr1	6264269	6394391	-
ACAP2	chr3	195274745	195443044	-
ADAR	chr1	154582057	154628013	-
AC118549.1	chr1	77562416	77683419	-
AC005943.1	chr19	1578339	1605445	-
ADA	chr20	44619522	44652233	-
ALDH7A1	chr5	126531200	126595362	-
AFG3L2	chr18	12328944	12377227	-
AL136295.1	chr14	24189157	24213473	-
ADORA1	chr1	203090654	203167405	+
ACTG1	chr17	81509971	81523847	-
ABCE1	chr4	145098288	145129524	+
AAGAB	chr15	67200667	67255195	-
ADARB1	chr21	45073853	45226560	+
ACSS3	chr12	80936414	81261210	+
ABHD8	chr19	17292131	17310236	-
ABHD10	chr3	111979010	111993368	+
ACTB	chr7	5527148	5563784	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-19a-3p	chr13	91350939	91350961	+
hsa-miR-19b-3p	chr13	91351245	91351267	+
hsa-miR-135b-5p	chr1	205448361	205448383	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC007566.1	chr7	92457564	92495601	+
AC010226.1	chr5	115602057	115623897	+
AC010442.1	chr5	466124	473098	-
AC012531.2	chr12	54017110	54035361	+
AC016876.2	chr17	7581964	7584086	-
AC023509.1	chr12	53441741	53467528	+
AC026461.1	chr16	56682470	56687807	+
AC064807.1	chr8	51899268	51949874	+
AC079781.5	chr7	97851688	97972985	-
AC099329.1	chr3	42785087	42852428	-
AC126365.1	chr17	20788071	20789584	+
AC132217.1	chr11	2129121	2129964	-
AD000090.1	chr19	35557956	35581954	+
AL096870.2	chr14	24209646	24215987	-

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.