exRNAdisease

General Information

Database ID:

exR0006591

RNA Name:

HSPA8

RNA Type:

mRNA

Chromosome:

chr11

Starnd:

Coordinate:

Start Site(bp):

123057489

End Site(bp):

123063230

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
ABCB4	chr7	87401697	87480435	-
AC018523.2	chr11	14493783	14520344	-
AC004922.1	chr7	99325879	99394653	+
ACBD5	chr10	27195214	27242130	-
AKIRIN1	chr1	38991276	39006059	+
AC008763.3	chr19	7678501	7682854	+
AC138811.2	chr16	18788063	18801519	-
ADSL	chr22	40346500	40390463	+
AC008758.1	chr19	12461559	12551474	-
ADM	chr11	10305073	10307397	+
AC009133.6	chr16	29812261	29820092	+
AC245033.1	chr15	82536788	82573194	-
ACTR1B	chr2	97655939	97664044	-
AFDN	chr6	167826922	167972023	+
ABCG2	chr4	88090150	88231628	-
AGPAT5	chr8	6708642	6761503	+
AKT1	chr14	104769349	104795751	-
ACTB	chr7	5527148	5563784	-
AL133352.1	chr10	100505628	100529881	-
ACAA2	chr18	49782164	49813953	-
AK4	chr1	65147549	65232145	+
AC091959.3	chr5	146203550	146339251	+
AGPAT3	chr21	43865223	43987592	+
ACTR2	chr2	65227753	65271253	+
AC139530.2	chr17	81703371	81720539	+
ACAT2	chr6	159762045	159779112	+
AL136295.4	chr14	24180395	24190416	-
AC091167.2	chr15	90249556	90272208	+
AL022238.4	chr22	40346529	40410054	+
ACTG1	chr17	81509971	81523847	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-155-5p	chr21	25573983	25574006	+
hsa-miR-302c-3p	chr4	112648366	112648388	-
hsa-miR-302a-5p	chr4	112648224	112648246	-
hsa-miR-632	chr17	32350169	32350187	+
hsa-miR-3654	chr7	133034860	133034878	-
hsa-miR-4485-3p	chr11	10508277	10508296	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC008555.5	chr19	34891605	34905139	-
AC012236.1	chr15	31221999	31230838	-
AC016876.2	chr17	7581964	7584086	-
AC040162.3	chr16	67882461	67886367	+
AC067852.2	chr17	42552436	42554748	-
AC106864.1	chr4	112693047	112706810	-
AC132217.1	chr11	2129121	2129964	-
AC245014.3	chr1	145281116	145281462	+
AD000090.1	chr19	35557956	35581954	+
AL022311.1	chr22	37876148	37895563	+
AL023653.1	chrX	129794994	129796963	+

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.