exRNAdisease

General Information

Database ID:

exR0000197

RNA Name:

ACTN1

RNA Type:

mRNA

Chromosome:

chr14

Starnd:

Coordinate:

Start Site(bp):

68874143

End Site(bp):

68979440

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
SLCO3A1	chr15	91853708	92172435	+
ATP5F1B	chr12	56638175	56645984	-
MT-CO2	chrMT	7586	8269	+
ZNF865	chr19	55605405	55617269	+
DPM2	chr9	127935099	127938484	-
G3BP1	chr5	151771045	151812785	+
ACTN3	chr11	66546395	66563334	+
VAT1	chr17	43014607	43025123	-
HMGN1	chr21	39342315	39349647	-
SUPT16H	chr14	21351476	21384019	-
PLPP3	chr1	56494761	56645301	-
ERG28	chr14	75649791	75660876	-
PKM	chr15	72199029	72231822	-
SPIN2B	chrX	57118551	57121546	-
NPC2	chr14	74476192	74494177	-
PFKL	chr21	44300051	44327376	+
FYN	chr6	111660332	111873452	-
FARP2	chr2	241356285	241494841	+
TRAF7	chr16	2155698	2178129	+
AC245033.1	chr15	82536788	82573194	-
SEC11A	chr15	84669538	84716460	-
HLA-B	chr6	31269491	31357188	-
DGCR8	chr22	20080232	20111877	+
CHTF8	chr16	69118010	69132578	-
ITFG2	chr12	2812622	2859791	+
POLL	chr10	101578882	101588270	-
POLB	chr8	42338454	42371808	+
ROCK1	chr18	20946906	21111813	-
CNOT1	chr16	58519951	58629885	-
PITPNA	chr17	1517718	1562792	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-367-3p	chr4	112647877	112647898	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC245033.4	chr15	82533175	82540008	-
BX284668.5	chr1	16887577	16889706	-

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.