exRNAdisease

General Information

Database ID:

exR0006381

RNA Name:

HLA-DRA

RNA Type:

mRNA

Chromosome:

chr6

Starnd:

Coordinate:

Start Site(bp):

32439878

End Site(bp):

32445046

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
AC104452.1	chr3	49416777	49429314	-
AL133352.1	chr10	100505628	100529881	-
AC010323.1	chr19	8308283	8321379	-
AC012254.2	chr18	47108188	47176345	-
AL136295.1	chr14	24189157	24213473	-
AC126283.2	chr4	109713916	109801999	-
AC010132.3	chr7	42909273	42932174	-
AFG3L2	chr18	12328944	12377227	-
ABHD10	chr3	111979010	111993368	+
AK2	chr1	33007940	33080996	-
ACSL4	chrX	109624244	109733403	-
ADPRHL2	chr1	36088892	36093932	+
AC011005.1	chr7	129126518	129130793	+
ACTR1B	chr2	97655939	97664044	-
AC007192.1	chr19	18153158	18178117	+
AC010422.6	chr19	12525720	12580975	-
ADRM1	chr20	62302093	62308862	+
AC011462.1	chr19	41350853	41425001	+
ACTR2	chr2	65227753	65271253	+
ABCF1	chr6	30571393	30597179	+
ABLIM1	chr10	114431113	114768061	-
ABCF2	chr7	151207837	151227166	-
AC004223.3	chr17	35011349	35121493	-
AC010547.4	chr16	71447600	71489311	-
ACADVL	chr17	7217125	7225266	+
ACTA1	chr1	229431245	229434098	-
ABHD17B	chr9	71862452	71910931	-
AKIRIN2	chr6	87674860	87702233	-
ACTB	chr7	5527148	5563784	-
AFDN	chr6	167826922	167972023	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-320a-3p	chr8	22244975	22244996	-
hsa-miR-155-5p	chr21	25573983	25574006	+
hsa-miR-155-3p	chr21	25574022	25574043	+
hsa-miR-3652	chr12	103930425	103930442	+
hsa-miR-3654	chr7	133034860	133034878	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC005899.4	chr17	32328441	32329395	+
AC007952.4	chr17	19112000	19112636	-
AC009403.1	chr7	155611231	155645205	-
AC009403.2	chr7	155474256	155644406	-
AC010969.2	chr2	9936360	9939590	+
AC022400.3	chr10	73674295	73730466	-
AC023509.1	chr12	53441741	53467528	+
AC026362.1	chr12	122975320	122982907	+
AC099778.1	chr3	47379089	47380999	-
AC245014.3	chr1	145281116	145281462	+
AD000090.1	chr19	35557956	35581954	+
AL022311.1	chr22	37876148	37895563	+
AL096870.2	chr14	24209646	24215987	-

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.