exRNAdisease

General Information

Database ID:

exR0012340

RNA Name:

RPL28

RNA Type:

mRNA

Chromosome:

chr19

Starnd:

Coordinate:

Start Site(bp):

55385345

End Site(bp):

55403250

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
ABCD3	chr1	94418389	94518666	+
AC004832.3	chr22	30409255	30428990	+
AC004922.1	chr7	99325879	99394653	+
AC005258.1	chr19	2269525	2341172	+
AC006064.6	chr12	6556886	6607367	-
AC010323.1	chr19	8308283	8321379	-
AC010422.3	chr19	12643831	12648397	-
AC024592.3	chr19	5866171	5903787	-
AC073508.2	chr17	40627356	40665141	-
AC093525.2	chr16	2496032	2520218	+
AC104389.5	chr11	5254392	5678434	-
AC138811.2	chr16	18788063	18801519	-
ACAT2	chr6	159762045	159779112	+
ACLY	chr17	41866917	41930542	-
ACO2	chr22	41469117	41528989	+
ACTA1	chr1	229431245	229434098	-
ACTB	chr7	5527148	5563784	-
ACTG1	chr17	81509971	81523847	-
ADGRL1	chr19	14147743	14206187	-
AEBP2	chr12	19404045	19720801	+
AGRN	chr1	1020120	1056118	+
AHCY	chr20	34280268	34311802	-
AKAP13	chr15	85380571	85749358	+
AL049629.2	chr11	33698261	33722467	-
AL669918.1	chr6	32813767	32838822	-
ALAS1	chr3	52198086	52214327	+
ALDH2	chr12	111766887	111817532	+
ALDOA	chr16	30064164	30070457	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-6805-5p	chr19	55388186	55388207	+
hsa-miR-6805-3p	chr19	55388220	55388242	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC007952.4	chr17	19112000	19112636	-
AC010327.5	chr19	55216660	55221616	+
AC012360.3	chr2	105334027	105337475	-
AC016747.1	chr2	61141592	61144969	-
AC020928.2	chr19	36773712	36775908	-
AC026362.1	chr12	122975320	122982907	+
AC026471.1	chr16	31456711	31459736	-
AC091564.7	chr11	6610883	6616594	-
AC139149.1	chr17	81514047	81527776	+
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.