exRNAdisease

General Information

Database ID:

exR0012394

RNA Name:

RPS17

RNA Type:

mRNA

Chromosome:

chr15

Starnd:

Coordinate:

Start Site(bp):

82536750

End Site(bp):

82540459

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
ABCA3	chr16	2275881	2340746	-
AC004832.3	chr22	30409255	30428990	+
AC007192.1	chr19	18153158	18178117	+
AC011005.1	chr7	129126518	129130793	+
AC011462.1	chr19	41350853	41425001	+
AC020909.1	chr19	50415799	50428409	+
AC024592.3	chr19	5866171	5903787	-
AC025165.3	chr12	57772660	57797554	+
AC245033.1	chr15	82536788	82573194	-
ACAD9	chr3	128879596	128916067	+
ACO2	chr22	41469117	41528989	+
ACTB	chr7	5527148	5563784	-
ACTC1	chr15	34790230	34795549	-
ACTN1	chr14	68874143	68979440	-
ACTN4	chr19	38647649	38731589	+
ACTR1A	chr10	102461881	102502712	-
ACTR3	chr2	113890063	113962596	+
ADO	chr10	62804720	62808479	+
AHCYL1	chr1	109984765	110023742	+
AK3	chr9	4709556	4742043	-
AL110118.2	chr14	93184973	93218586	+
AL121845.3	chr20	63708864	63739103	+
AL132780.3	chr14	22946270	22982258	-
AL133352.1	chr10	100505628	100529881	-
AL590764.2	chrX	71103987	71111575	-
AL603832.3	chr1	112702614	112711433	-
ALDOA	chr16	30064164	30070457	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-155-5p	chr21	25573983	25574006	+
hsa-miR-155-3p	chr21	25574022	25574043	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC016876.2	chr17	7581964	7584086	-
AC025181.2	chr5	32174471	32175272	+
AC026304.1	chr3	143000907	143001467	-
AC026362.1	chr12	122975320	122982907	+
AC087482.1	chr15	66984103	67065268	-
AC091564.7	chr11	6610883	6616594	-
AC114763.1	chr2	138418284	138501698	-
AC124312.5	chr15	25091786	25107469	-
AC132217.1	chr11	2129121	2129964	-
AC245033.4	chr15	82533175	82540008	-
AD000090.1	chr19	35557956	35581954	+

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.