exRNAdisease

General Information

Database ID:

exR0000047

RNA Name:

ABCC10

RNA Type:

mRNA

Chromosome:

chr6

Starnd:

Coordinate:

Start Site(bp):

43427366

End Site(bp):

43450427

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
GTPBP1	chr22	38705742	38738299	+
PUM1	chr1	30931506	31065991	-
ELMSAN1	chr14	73715122	73790285	-
ZNF462	chr9	106863166	107013634	+
RPL13	chr16	89560657	89566828	+
DIP2A	chr21	46458891	46570015	+
YWHAG	chr7	76326799	76358991	-
DNMT1	chr19	10133345	10231286	-
ERCC2	chr19	45349837	45370918	-
EGFL7	chr9	136658856	136672678	+
MAP3K11	chr11	65597756	65615382	-
RPL18A	chr19	17859910	17864153	+
CLEC2D	chr12	9664969	9699553	+
SPATA20	chr17	50543058	50555852	+
SLC12A9	chr7	100826820	100867010	+
DYRK2	chr12	67648338	67665406	+
SF3A2	chr19	2236824	2248655	+
NCOA6	chr20	34689097	34825651	-
PLCG1	chr20	41136960	41196801	+
FBN2	chr5	128257909	128659185	-
MCCC2	chr5	71587288	71658706	+
AP5B1	chr11	65773898	65780976	-
UBAC1	chr9	135932969	135961373	-
MMADHC	chr2	149569637	149587778	-
PKMYT1	chr16	2968024	2980479	-
UGP2	chr2	63840940	63891562	+
FAM3A	chrX	154506159	154516242	-
NOTCH2	chr1	119911553	120100779	-
IMP3	chr15	75639085	75648706	-
PHGDH	chr1	119648411	119744226	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-6780b-3p	chr6	43434600	43434620	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC007952.4	chr17	19112000	19112636	-
AC092139.1	chr16	81385463	81387560	+
AP001266.1	chr11	65795946	65797219	-
LINC01248	chr2	5602505	5691488	-

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.