exRNAdisease

General Information

Database ID:

exR0007887

RNA Name:

LMNB2

RNA Type:

mRNA

Chromosome:

chr19

Starnd:

Coordinate:

Start Site(bp):

2427638

End Site(bp):

2456959

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
AASS	chr7	122073549	122144255	-
ABI3	chr17	49210411	49223225	+
AC005258.1	chr19	2269525	2341172	+
AC008878.3	chr19	7382834	7470241	+
AC011448.1	chr19	19516227	19536076	+
AC138696.1	chr8	143247110	143276403	+
AC138811.2	chr16	18788063	18801519	-
AC138969.1	chr16	16317444	16350590	+
ACTB	chr7	5527148	5563784	-
ACTG1	chr17	81509971	81523847	-
ACTN4	chr19	38647649	38731589	+
ADAM11	chr17	44758988	44781846	+
ADD1	chr4	2843857	2930076	+
ADK	chr10	74151202	74709963	+
ADM2	chr22	50481543	50486440	+
AGAP1	chr2	235494043	236131800	+
AHCY	chr20	34280268	34311802	-
AHCYL2	chr7	129225023	129430211	+
AHSA1	chr14	77457870	77469472	+
AKAP17A	chrX	1591604	1602520	+
AKT1	chr14	104769349	104795751	-
AL021546.1	chr12	120438198	120460006	+
ALAS1	chr3	52198086	52214327	+
ALDH9A1	chr1	165662216	165698863	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-4485-3p	chr11	10508277	10508296	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AL022157.1	chrX	57121662	57127243	+
AL096828.3	chr20	63218041	63218502	+
AL117335.1	chr20	1888128	1894374	-
AL118516.1	chr22	46761894	46762563	-

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.