exRNAdisease

General Information

Database ID:

exR0000128

RNA Name:

ACBD5

RNA Type:

mRNA

Chromosome:

chr10

Starnd:

Coordinate:

Start Site(bp):

27195214

End Site(bp):

27242130

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
CDC42SE1	chr1	151050971	151070325	-
MAML3	chr4	139716753	140154184	-
TUBA1C	chr12	49188736	49274603	+
RPL13A	chr19	49487554	49492308	+
MAP4K2	chr11	64784918	64803241	-
PTCD1	chr7	99416739	99466163	-
ATP5MF-PTCD1	chr7	99419749	99466197	-
HSPA8	chr11	123057489	123063230	-
GGA2	chr16	23463542	23521995	-
TUBA1A	chr12	49184795	49189080	-
TMEM216	chr11	61392360	61398863	+
YLPM1	chr14	74763316	74859435	+
AMOT	chrX	112774503	112840815	-
IGF2	chr11	2129112	2141238	-
PLS1	chr3	142596393	142713664	+
DECR2	chr16	401858	412487	+
TPI1	chr12	6867119	6870948	+
RNF7	chr3	141738249	141747560	+
ENO1	chr1	8861000	8879190	-
RTN3	chr11	63681446	63759891	+
MYL12B	chr18	3261479	3278431	+
B2M	chr15	44711487	44718877	+
LRIG2	chr1	113073198	113132260	+
CKAP5	chr11	46743048	46846308	-
RPS24	chr10	78033760	78056813	+
GOT2	chr16	58707131	58734342	-
HIPK3	chr11	33256672	33357023	+
FTL	chr19	48965309	48966879	+
LCP1	chr13	46125920	46211871	-
NACA2	chr17	61590421	61591219	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-93-5p	chr7	100093815	100093837	-
hsa-miR-145-5p	chr5	149430661	149430683	+
hsa-miR-526b-5p	chr19	53694406	53694428	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC020916.1	chr19	13823880	13842928	-
AC132217.1	chr11	2129121	2129964	-
SNHG1	chr11	62851984	62855953	-

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.