exRNAdisease

General Information

Database ID:

exR0008404

RNA Name:

MCM7

RNA Type:

mRNA

Chromosome:

chr7

Starnd:

Coordinate:

Start Site(bp):

100092728

End Site(bp):

100101940

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
AAR2	chr20	36236459	36270918	+
AC010422.5	chr19	12664828	12669397	-
AC037459.1	chr8	22589274	22602084	+
AC073508.2	chr17	40627356	40665141	-
AC091551.1	chr18	50968019	51058144	+
AC131160.1	chr3	183815568	183884889	-
AC245033.1	chr15	82536788	82573194	-
ACADS	chr12	120725774	120740008	+
ACIN1	chr14	23058564	23095614	-
ACTN3	chr11	66546395	66563334	+
ACVR1B	chr12	51951699	51997078	+
ADAMTS1	chr21	26835755	26845409	-
ADD2	chr2	70607618	70768225	-
ADGRV1	chr5	90529344	91164437	+
ADPGK	chr15	72751369	72785846	-
AGO2	chr8	140520156	140635633	-
AHCY	chr20	34280268	34311802	-
AIF1L	chr9	131096476	131123152	+
AKT2	chr19	40230317	40285536	-
AL513165.2	chr9	37512547	37592469	-
ALDH18A1	chr10	95605941	95656711	-
ALDH9A1	chr1	165662216	165698863	-
ALDOA	chr16	30064164	30070457	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-93-5p	chr7	100093815	100093837	-
hsa-miR-25-5p	chr7	100093610	100093630	-
hsa-miR-6790-3p	chr19	6392925	6392945	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC004687.1	chr17	58330884	58332508	-
AC016876.2	chr17	7581964	7584086	-
AC091493.1	chr3	16687986	16697479	-
AC091564.7	chr11	6610883	6616594	-
AC106864.1	chr4	112693047	112706810	-
AC132217.1	chr11	2129121	2129964	-

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.