exRNAdisease

General Information

Database ID:

exR0006266

RNA Name:

HDLBP

RNA Type:

mRNA

Chromosome:

chr2

Starnd:

Coordinate:

Start Site(bp):

241227264

End Site(bp):

241317061

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
AAK1	chr2	69457997	69674349	-
AASS	chr7	122073549	122144255	-
AC002985.1	chr19	18907013	18934397	-
AC004922.1	chr7	99325879	99394653	+
AC011462.1	chr19	41350853	41425001	+
AC097637.1	chr3	52221081	52231190	-
ACACB	chr12	109116595	109268226	+
ACAD9	chr3	128879596	128916067	+
ACAT2	chr6	159762045	159779112	+
ACIN1	chr14	23058564	23095614	-
ACTR1B	chr2	97655939	97664044	-
ADH5	chr4	99070978	99088801	-
AHCY	chr20	34280268	34311802	-
AIMP2	chr7	6009255	6023834	+
AK3	chr9	4709556	4742043	-
AKR1A1	chr1	45550543	45570049	+
AKT2	chr19	40230317	40285536	-
AL138752.2	chr9	37588413	38068687	-
AL355987.3	chr9	136791379	136800595	+
ALDOA	chr16	30064164	30070457	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-let-7d-5p	chr9	94178841	94178862	+
hsa-let-7e-5p	chr19	51692793	51692814	+
hsa-let-7f-5p	chrX	53557246	53557267	-
hsa-miR-214-3p	chr1	172138816	172138837	-
hsa-let-7g-5p	chr3	52268336	52268357	-
hsa-let-7i-5p	chr12	62603691	62603712	+
hsa-miR-185-5p	chr22	20033153	20033174	+
hsa-miR-629-5p	chr15	70079427	70079447	-
hsa-miR-1321	chrX	85835832	85835849	+
hsa-miR-3652	chr12	103930425	103930442	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC016876.2	chr17	7581964	7584086	-
AD000090.1	chr19	35557956	35581954	+

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.