exRNAdisease

General Information

Database ID:

exR0000046

RNA Name:

ABCC1

RNA Type:

mRNA

Chromosome:

chr16

Starnd:

Coordinate:

Start Site(bp):

15949577

End Site(bp):

16143074

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
TMED2	chr12	123584533	123598582	+
PCDHGB6	chr5	141408021	141512979	+
ADGRV1	chr5	90529344	91164437	+
CENPU	chr4	184694085	184734130	-
RFC5	chr12	118013588	118033130	+
BLVRB	chr19	40447765	40465764	-
MACF1	chr1	39081316	39487177	+
RPS5	chr19	58386400	58394806	+
SETD1A	chr16	30957754	30984664	+
CRTC3	chr15	90529923	90645345	+
PCDHGB1	chr5	141350102	141512979	+
PCDHGA8	chr5	141390157	141512979	+
NUCKS1	chr1	205712822	205750182	-
MT-ND4	chrMT	10760	12137	+
ASXL1	chr20	32358330	32439319	+
STRBP	chr9	123109500	123268586	-
UBE2S	chr19	55399745	55407788	-
ZDHHC4	chr7	6577434	6589374	+
NOP53	chr19	47745546	47757058	+
CD52	chr1	26317958	26320523	+
PSMB9	chr6	32844136	32859851	+
PCDHGA7	chr5	141382739	141512975	+
MT-CYB	chrMT	14747	15887	+
MT-ND5	chrMT	12337	14148	+
PCDHGA6	chr5	141373914	141512979	+
PCDHGA5	chr5	141364232	141512979	+
EIF4G2	chr11	10797050	10808940	-
MT-CO2	chrMT	7586	8269	+
SC5D	chr11	121292681	121313410	+
AC104109.3	chr5	134167170	134226071	-

miRNA targets:

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AD000090.1	chr19	35557956	35581954	+
AL136419.1	chr14	23969931	24051377	+
AC138932.3	chr16	14909887	14911345	-
ERVK13-1	chr16	2660348	2682379	-
GAS5	chr1	173858559	173868882	-
MIR663AHG	chr20	26167817	26251546	-
SNHG17	chr20	38419638	38435409	-
SNHG19	chr16	2154797	2155358	-
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.