exRNAdisease

General Information

Database ID:

exR0000184

RNA Name:

ACTA1

RNA Type:

mRNA

Chromosome:

chr1

Starnd:

Coordinate:

Start Site(bp):

229431245

End Site(bp):

229434098

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
PRMT2	chr21	46635595	46665124	+
ACTR1B	chr2	97655939	97664044	-
SLC38A10	chr17	81244811	81295547	-
SNRPB2	chr20	16729961	16742564	+
AL136454.1	chr1	192716132	192716653	+
TARDBP	chr1	11012344	11026420	+
EIF5A	chr17	7306999	7312463	+
ATP5PD	chr17	75038863	75046985	-
LIX1L	chr1	145933423	145958017	-
SLC25A3	chr12	98593591	98606379	+
FTL	chr19	48965309	48966879	+
RPL28	chr19	55385345	55403250	+
POTEJ	chr2	130611481	130658091	+
AGGF1	chr5	77029251	77065234	+
MCM2	chr3	127598410	127622436	+
ERGIC3	chr20	35542021	35557634	+
HEXA	chr15	72340919	72376476	-
UBE4B	chr1	10032832	10181239	+
ACTC1	chr15	34790230	34795549	-
RPL23	chr17	38847860	38853764	-
SEC61G	chr7	54752250	54759974	-
MRPS27	chr5	72219409	72320646	-
RPL11	chr1	23691742	23696835	+
RNPEP	chr1	201982372	202006147	+
PFN1	chr17	4945652	4949061	-
PPIA	chr7	44796680	44824564	+
RPL36	chr19	5674947	5691875	+
POLR3C	chr1	145824088	145844402	+
TNIP1	chr5	151029945	151093577	-
CDC42SE1	chr1	151050971	151070325	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-4426	chr1	192716333	192716349	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AL022311.1	chr22	37876148	37895563	+
AL355472.2	chr1	234357006	234365828	+
AL359924.1	chr1	237862175	237928321	+
LINC00847	chr5	180830326	180839742	+

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.