exRNAdisease

General Information

Database ID:

exR0000385

RNA Name:

AGPS

RNA Type:

mRNA

Chromosome:

chr2

Starnd:

Coordinate:

Start Site(bp):

177392757

End Site(bp):

177559299

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
C2orf81	chr2	74414176	74421591	-
ZDHHC8	chr22	20129456	20148007	+
HES1	chr3	194136148	194138732	+
AP2M1	chr3	184174689	184184091	+
NDUFB11	chrX	47142216	47145504	-
RPS3A	chr4	151099624	151104642	+
NUDT15	chr13	48037726	48047221	+
HMGCR	chr5	75336329	75362101	+
OXA1L	chr14	22766522	22773042	+
RPL27A	chr11	8682788	8714759	+
RAB7A	chr3	128726183	128814798	+
RSRC2	chr12	122503454	122527000	-
CDCA7	chr2	173354820	173368997	+
DMWD	chr19	45782947	45792845	-
NCOR2	chr12	124324415	124567589	-
PSMC6	chr14	52707178	52728590	+
ATF4	chr22	39519695	39522685	+
EIF4G3	chr1	20806292	21176888	-
RPS24	chr10	78033760	78056813	+
ANAPC4	chr4	25377213	25418498	+
KHSRP	chr19	6413348	6424794	-
PSMB7	chr9	124353465	124415444	-
TRAP1	chr16	3651639	3717553	-
NCAPD2	chr12	6493356	6531955	+
FEZF2	chr3	62369681	62374324	-
ENO1	chr1	8861000	8879190	-
GPR176	chr15	39799008	39920266	-
HSPA4	chr5	133052013	133106449	+
RPL12	chr9	127447674	127451406	-
PARP2	chr14	20343582	20357905	+

miRNA targets:

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AL022311.1	chr22	37876148	37895563	+
AC138932.3	chr16	14909887	14911345	-
AP005263.1	chr18	9102736	9254346	+
LINC00910	chr17	43338741	43389199	-
LINC01641	chr1	227393554	227431035	+

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.