exRNAdisease

General Information

Database ID:

exR0000202

RNA Name:

ACTR1A

RNA Type:

mRNA

Chromosome:

chr10

Starnd:

Coordinate:

Start Site(bp):

102461881

End Site(bp):

102502712

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
ACTR1B	chr2	97655939	97664044	-
AP002990.1	chr11	62559603	62591531	-
PPP3R1	chr2	68178857	68256237	-
MT-ND3	chrMT	10059	10404	+
CDK19	chr6	110609978	110815958	-
ERC2	chr3	55508311	56468467	-
MT-ND1	chrMT	3307	4262	+
INO80	chr15	40978880	41116280	-
TCOF1	chr5	150357629	150400308	+
OS9	chr12	57693955	57721557	+
GOLGA7	chr8	41490396	41510980	+
PAPOLA	chr14	96501433	96567111	+
IGFBP2	chr2	216632828	216664436	+
RPL27A	chr11	8682788	8714759	+
PDE7A	chr8	65717510	65842322	-
RPS6	chr9	19375715	19380236	-
HNRNPL	chr19	38836388	38852347	-
MT-ND4	chrMT	10760	12137	+
EIF5AL1	chr10	79512601	79516440	+
COMMD10	chr5	116085016	116412762	+
TMSB4X	chrX	12975110	12977227	+
RPL29	chr3	51993522	51995895	-
CBSL	chr21	6444869	6468040	-
GGCT	chr7	30496621	30504841	-
ARHGEF19	chr1	16197854	16212652	-
SAE1	chr19	47113274	47210636	+
TRIM28	chr19	58544064	58550722	+
CHST14	chr15	40470998	40474571	+
TBCB	chr19	36114289	36125947	+
CREBL2	chr12	12611827	12645108	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-363-3p	chrX	134169382	134169403	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC011297.1	chrY	6918682	6920791	+
AC027020.2	chr15	100547765	100550153	-
AC245014.3	chr1	145281116	145281462	+
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.