exRNAdisease

General Information

Database ID:

exR0003866

RNA Name:

DHCR24

RNA Type:

mRNA

Chromosome:

chr1

Starnd:

Coordinate:

Start Site(bp):

54849627

End Site(bp):

54887195

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
ABL1	chr9	130713016	130887675	+
AC004832.3	chr22	30409255	30428990	+
AC005258.1	chr19	2269525	2341172	+
AC008763.3	chr19	7678501	7682854	+
AC091167.2	chr15	90249556	90272208	+
AC120057.2	chr17	7240427	7244635	-
ACADSB	chr10	123008979	123058290	+
ACIN1	chr14	23058564	23095614	-
ACTA1	chr1	229431245	229434098	-
ADAR	chr1	154582057	154628013	-
ADGRA3	chr4	22345071	22516066	-
AK2	chr1	33007940	33080996	-
AKIRIN1	chr1	38991276	39006059	+
AKR1B1	chr7	134442356	134459284	-
AL136295.1	chr14	24189157	24213473	-
AL713999.1	chr1	155169409	155187272	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-7-5p	chr19	4770700	4770723	+
hsa-miR-654-5p	chr14	101040234	101040255	+
hsa-miR-541-3p	chr14	101064548	101064569	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC006064.5	chr12	6510275	6510522	+
AC016876.2	chr17	7581964	7584086	-
AC040162.3	chr16	67882461	67886367	+
AC244517.11	chr5	141136683	141245380	-
AD000090.1	chr19	35557956	35581954	+
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.