exRNAdisease

General Information

Database ID:

exR0000062

RNA Name:

ABCF1

RNA Type:

mRNA

Chromosome:

chr6

Starnd:

Coordinate:

Start Site(bp):

30571393

End Site(bp):

30597179

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
HLA-DRB1	chr6	32578769	32589848	-
ZNF501	chr3	44729596	44737083	+
TMEM250	chr9	136114581	136118875	-
MT-CO1	chrMT	5904	7445	+
GLUL	chr1	182381704	182392206	-
CIC	chr19	42268537	42295797	+
MTRNR2L8	chr11	10507894	10509186	-
MYLIP	chr6	16129086	16148248	+
IFIT3	chr10	89327997	89340971	+
ZNF581	chr19	55635459	55645623	+
MAU2	chr19	19320829	19358754	+
CERS2	chr1	150960583	150975004	-
TNRC6A	chr16	24610209	24827632	+
PDP2	chr16	66878589	66895754	+
BSG	chr19	571277	583493	+
EEF1G	chr11	62559596	62574086	-
PTBP1	chr19	797075	812327	+
AP1S2	chrX	15825806	15854931	-
FTL	chr19	48965309	48966879	+
IQGAP1	chr15	90388242	90502239	+
SURF4	chr9	133361450	133376166	-
SELENON	chr1	25800176	25818221	+
RPS6	chr9	19375715	19380236	-
PDCD6IP	chr3	33798571	33869707	+
GPC6	chr13	93226807	94408020	+
VPS26A	chr10	69123512	69174412	+
CYFIP2	chr5	157266079	157395595	+
MFSD5	chr12	53251251	53254405	+
AC005832.4	chr12	4604944	4662643	+
BZW2	chr7	16646131	16706523	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-302c-3p	chr4	112648366	112648388	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC000068.1	chr22	19447893	19450105	+
AC010642.2	chr19	58309727	58327248	-
DANCR	chr4	52712404	52720351	+

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.