exRNAdisease

General Information

Database ID:

exR0000129

RNA Name:

ACBD6

RNA Type:

mRNA

Chromosome:

chr1

Starnd:

Coordinate:

Start Site(bp):

180269653

End Site(bp):

180502954

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
TMEM187	chrX	153972754	153983194	+
SIGMAR1	chr9	34634722	34637809	-
COPS7A	chr12	6724014	6731875	+
SPTLC3	chr20	13008972	13169103	+
BLOC1S1	chr12	55716037	55720087	+
TOB2	chr22	41433494	41446801	-
ACAP3	chr1	1292390	1309609	-
AC011455.2	chr19	38915404	38949855	-
TUBA1A	chr12	49184795	49189080	-
GLTP	chr12	109850945	109880541	-
FBXO17	chr19	38941401	38975742	-
CMTM4	chr16	66614750	66696707	-
AC055811.2	chr17	17202649	17237185	-
PHACTR4	chr1	28369582	28500364	+
NUDT15	chr13	48037726	48047221	+
ADGRL1	chr19	14147743	14206187	-
RER1	chr1	2391775	2405442	+
EIF4H	chr7	74174245	74197101	+
MAFK	chr7	1530702	1543043	+
PLXNA3	chrX	154458281	154477779	+
TOMM40	chr19	44890569	44903689	+
HAUS1	chr18	46104378	46128333	+
INPP5A	chr10	132537787	132783480	+
FTL	chr19	48965309	48966879	+
HINFP	chr11	119121580	119136059	+
MT-CO2	chrMT	7586	8269	+
TUBB	chr6	30720352	30725426	+
SEH1L	chr18	12947133	12987536	+
VCP	chr9	35056064	35072627	-
B3GNT5	chr3	183253253	183298504	+

miRNA targets:

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AL121992.1	chr1	15586136	15603626	-
AL121987.1	chr1	160062461	160080769	+
AL645608.2	chr1	911435	914948	+
MALAT1	chr11	65497688	65506516	+
SLC16A1-AS1	chr1	112956415	113047055	+

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.