exRNAdisease

General Information

Database ID:

exR0000064

RNA Name:

ABCF3

RNA Type:

mRNA

Chromosome:

chr3

Starnd:

Coordinate:

Start Site(bp):

184186023

End Site(bp):

184194012

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
STARD10	chr11	72754729	72793681	-
TRIOBP	chr22	37697048	37776556	+
ABCF2	chr7	151207837	151227166	-
AFDN	chr6	167826922	167972023	+
MBD5	chr2	148021011	148516971	+
RARB	chr3	25174332	25597932	+
EPN3	chr17	50532682	50543750	+
TPI1	chr12	6867119	6870948	+
PPP1R16B	chr20	38805697	38923024	+
MATR3	chr5	139273752	139331671	+
RAB43	chr3	129087569	129122801	-
EXOC7	chr17	76081016	76121576	-
SSR4	chrX	153793516	153798499	+
RPS19	chr19	41860255	41872925	+
ZEB2	chr2	144364364	144521057	-
HOXD3	chr2	176136612	176173102	+
KRR1	chr12	75490863	75511636	-
LIG3	chr17	34980512	35009743	+
Z83844.1	chr22	37686414	37726503	+
RPL13	chr16	89560657	89566828	+
SNRPG	chr2	70281362	70293740	-
EEF1A1	chr6	73515750	73523797	-
PDCD7	chr15	65117379	65133808	-
MAPKAP1	chr9	125437393	125707234	-
RPS6	chr9	19375715	19380236	-
GGA3	chr17	75236599	75262363	-
RERE	chr1	8352397	8848921	-
SAT1	chrX	23783173	23786226	+
MTRNR2L12	chr3	96617188	96618236	-
MARCKSL1	chr1	32333839	32336233	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-15a-5p	chr13	50049167	50049188	-
hsa-miR-15b-5p	chr3	160404607	160404628	+
hsa-miR-34c-5p	chr11	111513451	111513473	+
hsa-miR-497-5p	chr17	7017979	7017999	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC016949.1	chr3	196912646	196914579	+
AL355075.4	chr14	20343048	20343685	-
LINC00858	chr10	84267747	84294659	+
RMRP	chr9	35657751	35658018	-
SRRM2-AS1	chr16	2737076	2752600	-
XIST	chrX	73820649	73852723	-

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.