exRNAdisease

General Information

Database ID:

exR0010554

RNA Name:

PGAM1

RNA Type:

mRNA

Chromosome:

chr10

Starnd:

Coordinate:

Start Site(bp):

97426191

End Site(bp):

97433444

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
AASDHPPT	chr11	106075501	106098699	+
ABCB6	chr2	219209772	219218994	-
ABHD17C	chr15	80679684	80755621	+
ABI2	chr2	203328239	203447728	+
ABL2	chr1	179099330	179229684	-
AC007846.2	chr17	5772926	6080792	+
AC073082.1	chr2	48632291	48755724	-
AC091959.3	chr5	146203550	146339251	+
AC110275.1	chr8	43018424	43077334	+
AC139530.2	chr17	81703371	81720539	+
AC245033.1	chr15	82536788	82573194	-
ACACA	chr17	37084992	37406836	-
ACAT2	chr6	159762045	159779112	+
ACBD7	chr10	15075475	15088776	-
ACTB	chr7	5527148	5563784	-
ACTR1A	chr10	102461881	102502712	-
ACTR1B	chr2	97655939	97664044	-
ADA	chr20	44619522	44652233	-
ADAR	chr1	154582057	154628013	-
ADD2	chr2	70607618	70768225	-
AFAP1	chr4	7758714	7939926	-
AGBL5	chr2	27042364	27070622	+
AKT2	chr19	40230317	40285536	-
AL024498.2	chr6	10747794	10930423	+
AL157392.5	chr10	13610047	13655929	+
ALDH18A1	chr10	95605941	95656711	-
ALDOA	chr16	30064164	30070457	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-423-5p	chr17	30117095	30117117	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC009022.1	chr16	69976297	70065948	-
AC026461.1	chr16	56682470	56687807	+
AC245033.4	chr15	82533175	82540008	-
AL022311.1	chr22	37876148	37895563	+

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.