exRNAdisease

General Information

Database ID:

exR0000187

RNA Name:

ACTC1

RNA Type:

mRNA

Chromosome:

chr15

Starnd:

Coordinate:

Start Site(bp):

34790230

End Site(bp):

34795549

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
SLC12A6	chr15	34229784	34338060	-
PRKDC	chr8	47773111	47960178	-
POTEI	chr2	130459455	130509707	-
VAT1	chr17	43014607	43025123	-
IL16	chr15	81159575	81314058	+
PCNA	chr20	5114953	5126626	-
FAM185A	chr7	102748971	102809225	+
RPS17	chr15	82536750	82540459	-
EDC3	chr15	74630558	74696292	-
TBC1D9B	chr5	179862066	179907859	-
ZBTB45	chr19	58513530	58538911	-
B2M	chr15	44711487	44718877	+
EID1	chr15	48878134	48880173	+
ENO2	chr12	6913745	6923698	+
UBQLN4	chr1	156035299	156053798	-
ATP1A1	chr1	116372668	116410261	+
AP1G1	chr16	71729000	71809201	-
SNRPB	chr20	2461634	2470853	-
RPL26	chr17	8377516	8383213	-
G6PD	chrX	154531391	154547572	-
CAND1	chr12	67269358	67319953	+
TPI1	chr12	6867119	6870948	+
AC245033.1	chr15	82536788	82573194	-
ACTR1A	chr10	102461881	102502712	-
CASC4	chr15	44288719	44415758	+
ACTA1	chr1	229431245	229434098	-
SORL1	chr11	121452314	121633763	+
JTB	chr1	153974269	153977674	-
VPS51	chr11	65089324	65111862	+
SERF2	chr15	43777087	43802589	+

miRNA targets:

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC019205.1	chr6	73263212	73301789	+
AC105339.2	chr15	82752884	82757208	+
AC139149.1	chr17	81514047	81527776	+
AC012379.1	chr15	48783190	48784121	+
AC135178.2	chr17	8318088	8318712	-
AL359924.1	chr1	237862175	237928321	+

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.