exRNAdisease

General Information

Database ID:

exR0006379

RNA Name:

HLA-DQB1

RNA Type:

mRNA

Chromosome:

chr6

Starnd:

Coordinate:

Start Site(bp):

32659467

End Site(bp):

32668383

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
AC008982.1	chr19	38817471	38840178	-
AC010422.3	chr19	12643831	12648397	-
AC087289.3	chr17	75898645	75930129	-
AC137834.1	chr12	57249609	57296484	-
AC245033.1	chr15	82536788	82573194	-
ACACA	chr17	37084992	37406836	-
ACLY	chr17	41866917	41930542	-
ACO1	chr9	32384603	32454769	+
ACOT7	chr1	6264269	6394391	-
ACTB	chr7	5527148	5563784	-
ACTG1	chr17	81509971	81523847	-
ACTR3	chr2	113890063	113962596	+
ADNP	chr20	50888916	50931437	-
ADORA2A	chr22	24417879	24442357	+
ADPRHL2	chr1	36088892	36093932	+
ADSL	chr22	40346500	40390463	+
AGPAT5	chr8	6708642	6761503	+
AHCY	chr20	34280268	34311802	-
AK2	chr1	33007940	33080996	-
AKAP13	chr15	85380571	85749358	+
AKIRIN1	chr1	38991276	39006059	+
AKR7A2	chr1	19303965	19312146	-
AL022238.4	chr22	40346529	40410054	+
AL669918.1	chr6	32813767	32838822	-
AL928654.3	chr14	105487199	105492267	+
ALDOA	chr16	30064164	30070457	+

miRNA targets:

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC008957.1	chr5	36666214	36725195	-
AC016876.2	chr17	7581964	7584086	-
AC109460.3	chr16	28974804	28990775	+
AC245033.4	chr15	82533175	82540008	-

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.