exRNAdisease

General Information

Database ID:

exR0010758

RNA Name:

PKM

RNA Type:

mRNA

Chromosome:

chr15

Starnd:

Coordinate:

Start Site(bp):

72199029

End Site(bp):

72231822

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	+
AC027796.3	chr17	3585149	3636249	-
AC091167.2	chr15	90249556	90272208	+
ACACB	chr12	109116595	109268226	+
AL136454.1	chr1	192716132	192716653	+
AC093525.2	chr16	2496032	2520218	+
AL121594.1	chr14	35122549	35317474	+
AHCY	chr20	34280268	34311802	-
ACADM	chr1	75724347	75787575	+
ADA	chr20	44619522	44652233	-
AKT1S1	chr19	49869033	49878459	-
ADAR	chr1	154582057	154628013	-
ACTG2	chr2	73892314	73919865	+
AASS	chr7	122073549	122144255	-
AL121753.1	chr20	35267885	35280043	-
ADAM22	chr7	87934143	88202889	+
AHNAK	chr11	62433542	62556235	-
ADPGK	chr15	72751369	72785846	-
AC011448.1	chr19	19516227	19536076	+
ACO2	chr22	41469117	41528989	+
AC011462.1	chr19	41350853	41425001	+
AC093323.1	chr4	6663396	6676755	+
AD000671.2	chr19	35739252	35745432	-
ACTG1	chr17	81509971	81523847	-
ACTC1	chr15	34790230	34795549	-
ACAT2	chr6	159762045	159779112	+
AL133352.1	chr10	100505628	100529881	-
AIP	chr11	67483026	67491103	+
AC010422.3	chr19	12643831	12648397	-
AF241726.2	chrX	37349330	38687674	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-103a-3p	chr5	168560904	168560926	-
hsa-miR-367-3p	chr4	112647877	112647898	-
hsa-miR-654-5p	chr14	101040234	101040255	+
hsa-miR-541-3p	chr14	101064548	101064569	+
hsa-miR-1286	chr22	20249145	20249165	-
hsa-miR-3610	chr8	116874740	116874759	-
hsa-miR-5587-5p	chr16	535316	535333	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC005899.4	chr17	32328441	32329395	+
AC010327.5	chr19	55216660	55221616	+
AC016876.2	chr17	7581964	7584086	-
AC020663.1	chr16	4730115	4752565	-
AC020928.1	chr19	36773112	36777078	+
AC024940.6	chr12	31280422	31280895	-
AC068205.2	chr11	43578889	43840030	+
AC079781.5	chr7	97851688	97972985	-
AC093827.4	chr4	86924630	86936202	-
AC100861.1	chr8	23224471	23230926	+
AC104461.1	chr1	200333193	200478669	+
AC106875.1	chr2	11681460	11683328	+
AC109460.3	chr16	28974804	28990775	+
AC132217.1	chr11	2129121	2129964	-
AC135048.1	chr16	30948386	30956511	+
AD000090.1	chr19	35557956	35581954	+
AL022311.1	chr22	37876148	37895563	+
AL031282.2	chr1	1702736	1737688	-
AL049796.1	chr1	93847174	93848939	+
AL110115.2	chr20	31580890	31581214	+
AL121992.1	chr1	15586136	15603626	-
AL137058.2	chr13	52600042	52642542	+

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.