exRNAdisease

General Information

Database ID:

exR0000063

RNA Name:

ABCF2

RNA Type:

mRNA

Chromosome:

chr7

Starnd:

Coordinate:

Start Site(bp):

151207837

End Site(bp):

151227166

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
COX7C	chr5	86617928	86620962	+
ABCF2	chr7	151207837	151227166	-
EIF3L	chr22	37848868	37889407	+
PROM1	chr4	15963076	16084378	-
MTG1	chr10	133394094	133422520	+
SPG11	chr15	44562696	44663678	-
SUV39H2	chr10	14878820	14904315	+
MAP4	chr3	47850690	48089272	-
BTBD2	chr19	1985438	2034881	-
TRAPPC12	chr2	3379675	3485094	+
DYNLL2	chr17	58083419	58095542	+
IL32	chr16	3065297	3082192	+
STAT5B	chr17	42199177	42276707	-
RPS4X	chrX	72255679	72277248	-
MCOLN1	chr19	7522624	7534009	+
OST4	chr2	27070472	27071654	-
SERPINE1	chr7	101127104	101139247	+
CCT4	chr2	61868085	61888671	-
ENO1	chr1	8861000	8879190	-
ELOVL5	chr6	53267398	53349179	-
CD164	chr6	109366514	109382467	-
SLC37A4	chr11	119024114	119030906	-
AL360181.3	chr10	133380017	133420271	+
PHIP	chr6	78934419	79078254	-
LPGAT1	chr1	211743457	211830763	-
BCAT2	chr19	48795062	48811029	-
UBB	chr17	16380798	16382745	+
ERMP1	chr9	5765076	5833117	-
UBE2Q1	chr1	154548577	154559028	-
SNRNP40	chr1	31259568	31296788	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-103a-3p	chr5	168560904	168560926	-
hsa-miR-107	chr10	89592756	89592778	-
hsa-miR-625-5p	chr14	65471116	65471136	+
hsa-miR-423-5p	chr17	30117095	30117117	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC005487.1	chr7	108598352	108639349	+
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.