exRNAdisease

General Information

Database ID:

exR0010568

RNA Name:

PGK1

RNA Type:

mRNA

Chromosome:

chrX

Starnd:

Coordinate:

Start Site(bp):

77910739

End Site(bp):

78129295

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
AIFM2	chr10	70098223	70132934	-
AC012254.2	chr18	47108188	47176345	-
AKIRIN2	chr6	87674860	87702233	-
AHSA1	chr14	77457870	77469472	+
AC011005.1	chr7	129126518	129130793	+
ADPGK	chr15	72751369	72785846	-
AKIRIN1	chr1	38991276	39006059	+
ABCC5	chr3	183919934	184017939	-
ABCB7	chrX	75051048	75156732	-
AFF4	chr5	132875395	132963634	-
ADCY5	chr3	123282296	123449758	-
AL121753.1	chr20	35267885	35280043	-
AC010422.5	chr19	12664828	12669397	-
AGGF1	chr5	77029251	77065234	+
ACTG1	chr17	81509971	81523847	-
ADGRB2	chr1	31727117	31764893	-
ABCE1	chr4	145098288	145129524	+
ACTR3	chr2	113890063	113962596	+
AC023055.1	chr12	55757275	55827546	-
AL355987.1	chr9	136738167	136748453	-
ADH5	chr4	99070978	99088801	-
ACAT1	chr11	108116695	108147603	+
AC008581.2	chr5	77030902	77152155	+
AFTPH	chr2	64524305	64593005	+
AAMP	chr2	218264123	218270257	-
ALDOA	chr16	30064164	30070457	+
ACTB	chr7	5527148	5563784	-
AL133352.1	chr10	100505628	100529881	-
ALDH3A2	chr17	19648136	19685760	+
AGFG1	chr2	227472152	227561214	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-29b-3p	chr7	130877467	130877489	-
hsa-miR-30c-5p	chr6	71377003	71377025	-
hsa-miR-136-5p	chr14	100884716	100884738	+
hsa-miR-299-3p	chr14	101023832	101023853	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC000068.1	chr22	19447893	19450105	+
AC007952.4	chr17	19112000	19112636	-
AC020663.1	chr16	4730115	4752565	-
AC023509.1	chr12	53441741	53467528	+
AC048341.2	chr12	62603909	62604399	+
AC074183.1	chr7	84939349	84940245	-
AC079781.5	chr7	97851688	97972985	-
AC091132.5	chr17	45549781	45558738	-
AC106864.1	chr4	112693047	112706810	-
AC113189.4	chr17	7439506	7445966	+
AC132217.1	chr11	2129121	2129964	-
AC133644.3	chr2	87455476	87767359	+
AL022311.1	chr22	37876148	37895563	+
AL137026.2	chr10	44259602	44261813	-

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.