exRNAdisease

General Information

Database ID:

exR0000200

RNA Name:

ACTN4

RNA Type:

mRNA

Chromosome:

chr19

Starnd:

Coordinate:

Start Site(bp):

38647649

End Site(bp):

38731589

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
NUP58	chr13	25301556	25349800	+
ID1	chr20	31605283	31606515	+
SAPCD1	chr6	31762996	31764851	+
SNRNP200	chr2	96274338	96321271	-
HSPA1A	chr6	31815543	31817946	+
MAN1C1	chr1	25617468	25786207	+
IREB2	chr15	78437431	78501453	+
CIB2	chr15	78104606	78131535	-
CRNKL1	chr20	20034368	20056046	-
TMEM158	chr3	45224466	45226287	-
AC020915.5	chr19	58228914	58315183	+
GCNT1	chr9	76419850	76651203	+
ATIC	chr2	215311956	215349773	+
VAPA	chr18	9914002	9960021	+
YWHAQ	chr2	9583967	9630997	-
CHD9	chr16	53055033	53329150	+
LRRD1	chr7	92141643	92179531	-
RAD23B	chr9	107283137	107332192	+
CFL1	chr11	65823022	65862026	-
STX10	chr19	13144058	13150383	-
PRRC2B	chr9	131373636	131500197	+
MTRNR2L8	chr11	10507894	10509186	-
HNRNPA2B1	chr7	26173057	26201529	-
BSPRY	chr9	113349541	113371233	+
ZFHX4	chr8	76681239	76867281	+
PTPN6	chr12	6946468	6961316	+
SET	chr9	128683424	128696400	+
NEDD8	chr14	24216857	24232367	-
PHLDB3	chr19	43474954	43504935	-
PKM	chr15	72199029	72231822	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-138-5p	chr16	56858527	56858549	+
hsa-miR-185-5p	chr22	20033153	20033174	+
hsa-miR-296-5p	chr20	58817661	58817681	-
hsa-miR-654-5p	chr14	101040234	101040255	+
hsa-miR-423-5p	chr17	30117095	30117117	+
hsa-miR-483-5p	chr11	2134181	2134202	-
hsa-miR-1286	chr22	20249145	20249165	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC010997.3	chr10	75279726	75401246	-
AC016876.2	chr17	7581964	7584086	-
AC026304.1	chr3	143000907	143001467	-
AC132217.1	chr11	2129121	2129964	-
AC245014.3	chr1	145281116	145281462	+
AC245033.4	chr15	82533175	82540008	-
AD000090.1	chr19	35557956	35581954	+
AC008731.1	chr16	24803451	24819739	-
AC020915.1	chr19	58278966	58315197	+
AC093734.1	chr7	1508655	1509427	-
AC135178.2	chr17	8318088	8318712	-
AL355075.4	chr14	20343048	20343685	-
GHRLOS	chr3	10285754	10294903	+
LIMD1-AS1	chr3	45676369	45689200	-
RMRP	chr9	35657751	35658018	-
SLC9A3-AS1	chr5	473236	480884	+
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.