exRNAdisease

General Information

Database ID:

exR0000324

RNA Name:

ADPGK

RNA Type:

mRNA

Chromosome:

chr15

Starnd:

Coordinate:

Start Site(bp):

72751369

End Site(bp):

72785846

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
EEF1A1	chr6	73515750	73523797	-
B4GAT1	chr11	66345374	66347629	-
MKNK2	chr19	2037465	2051244	-
UBA2	chr19	34428352	34471251	+
PGK1	chrX	77910739	78129295	+
STAMBP	chr2	73828916	73873659	+
CCDC150	chr2	196639554	196763490	+
SRSF1	chr17	58000919	58007346	-
GTF3C2	chr2	27325849	27357034	-
EIF3H	chr8	116642130	116766925	-
ACTB	chr7	5527148	5563784	-
GMCL1	chr2	69829660	69881384	+
BCAR3	chr1	93561741	93847150	-
UBE2V2	chr8	48008415	48064708	+
MTHFD2	chr2	74198610	74217565	+
MT-CO1	chrMT	5904	7445	+
NOL8	chr9	92297358	92325636	-
EFTUD2	chr17	44849948	44899445	-
PPP1R14B	chr11	64244479	64246943	-
ZFP42	chr4	187995771	188005046	+
ATG4B	chr2	241637213	241673857	+
NDUFB3	chr2	201071433	201085750	+
BCKDK	chr16	31106107	31112791	+
PCBP2	chr12	53452102	53481162	+
MORC4	chrX	106813871	107000212	-
HMGB2	chr4	173331376	173334432	-
SLC25A29	chr14	100291116	100306547	-
TBCA	chr5	77691166	77868780	-
SACS	chr13	23328826	23433740	-
PASK	chr2	241106099	241150264	-

miRNA targets:

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC016876.2	chr17	7581964	7584086	-
AC023509.1	chr12	53441741	53467528	+
AC135050.1	chr16	31056460	31062803	+
AL355488.1	chr1	110370154	110373003	+
PCBP2-OT1	chr12	53464468	53465057	+
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.