exRNAdisease

General Information

Database ID:

exR0006369

RNA Name:

HLA-B

RNA Type:

mRNA

Chromosome:

chr6

Starnd:

Coordinate:

Start Site(bp):

31269491

End Site(bp):

31357188

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
ACTA2	chr10	88935074	88991339	-
ACTG1	chr17	81509971	81523847	-
ADPRHL2	chr1	36088892	36093932	+
AK4	chr1	65147549	65232145	+
AC092647.5	chr7	55887277	55955239	+
ADM	chr11	10305073	10307397	+
AHCY	chr20	34280268	34311802	-
ACTB	chr7	5527148	5563784	-
ABCC10	chr6	43427366	43450427	+
ACOT7	chr1	6264269	6394391	-
ADAR	chr1	154582057	154628013	-
AGTRAP	chr1	11736084	11754802	+
ADI1	chr2	3497366	3519531	-
AK2	chr1	33007940	33080996	-
ABLIM1	chr10	114431113	114768061	-
AC069503.2	chr12	121888809	121921470	+
AL109827.1	chr20	35632340	35674544	-
AGAP3	chr7	151085831	151144436	+
AC011462.1	chr19	41350853	41425001	+
AC135050.2	chr16	31083439	31094956	-
AC046185.1	chr17	63702845	63752097	-
ADRM1	chr20	62302093	62308862	+
AC010422.3	chr19	12643831	12648397	-
AC005258.1	chr19	2269525	2341172	+
ADGRG2	chrX	18989307	19122637	-
ACTR3	chr2	113890063	113962596	+
ADCY1	chr7	45574140	45723116	+
ACTA1	chr1	229431245	229434098	-
ACADSB	chr10	123008979	123058290	+
AICDA	chr12	8602170	8612867	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-155-5p	chr21	25573983	25574006	+
hsa-miR-6891-5p	chr6	31355297	31355315	-
hsa-miR-6516-5p	chr17	77089428	77089449	+
hsa-miR-6516-3p	chr17	77089469	77089490	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC002470.2	chr22	20979462	20998121	+
AC006942.1	chr19	49808933	49809738	+
AC019205.1	chr6	73263212	73301789	+
AC023509.1	chr12	53441741	53467528	+
AC067852.2	chr17	42552436	42554748	-
AC091564.7	chr11	6610883	6616594	-
AC093157.1	chr1	101025844	101090513	+
AC134043.2	chr5	159209921	159248796	+
AC139530.1	chr17	81701324	81703300	-
AC147651.4	chr7	603185	608482	+

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.