exRNAdisease

General Information

Database ID:

exR0013937

RNA Name:

SRRM2

RNA Type:

mRNA

Chromosome:

chr16

Starnd:

Coordinate:

Start Site(bp):

2752626

End Site(bp):

2772538

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
ABCA2	chr9	137007234	137028922	-
ABCB8	chr7	151028422	151047782	+
ABCG2	chr4	88090150	88231628	-
ABI1	chr10	26746593	26861087	-
ABT1	chr6	26596953	26600739	+
AC010422.3	chr19	12643831	12648397	-
AC046185.1	chr17	63702845	63752097	-
AC092143.1	chr16	89919165	89936092	+
AC093525.1	chr16	2513965	2527955	+
AC104452.1	chr3	49416777	49429314	-
AC107871.1	chr15	68184032	68229718	-
AC120057.2	chr17	7240427	7244635	-
AC138811.2	chr16	18788063	18801519	-
ACTB	chr7	5527148	5563784	-
ACTN4	chr19	38647649	38731589	+
ADAM10	chr15	58588809	58749791	-
ADAM15	chr1	155050566	155062775	+
ADGRE5	chr19	14380501	14408725	+
ADGRL2	chr1	81306160	81992436	+
ADRM1	chr20	62302093	62308862	+
AGGF1	chr5	77029251	77065234	+
AGPAT1	chr6	32168212	32178096	-
AHNAK	chr11	62433542	62556235	-
AK4	chr1	65147549	65232145	+
AKT2	chr19	40230317	40285536	-
ALDH18A1	chr10	95605941	95656711	-
ALDOA	chr16	30064164	30070457	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-3648	chr21	8987026	8987046	+
hsa-miR-7847-3p	chr11	1880105	1880125	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC005696.4	chr17	2720801	2723947	-
AC007952.4	chr17	19112000	19112636	-
AC016876.2	chr17	7581964	7584086	-
AC020663.1	chr16	4730115	4752565	-
AC026362.1	chr12	122975320	122982907	+
AC051619.7	chr15	45200325	45200632	-
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.