exRNAdisease

General Information

Database ID:

exR0002383

RNA Name:

CD74

RNA Type:

mRNA

Chromosome:

chr5

Starnd:

Coordinate:

Start Site(bp):

150400041

End Site(bp):

150412929

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
AKT1	chr14	104769349	104795751	-
A4GALT	chr22	42692121	42721298	-
ACTN4	chr19	38647649	38731589	+
AHCY	chr20	34280268	34311802	-
ACTG1	chr17	81509971	81523847	-
AATF	chr17	36948954	37056871	+
AC006064.6	chr12	6556886	6607367	-
AC005258.1	chr19	2269525	2341172	+
AHCYL1	chr1	109984765	110023742	+
AC023055.1	chr12	55757275	55827546	-
AKAP8	chr19	15353385	15379798	-
ALDOA	chr16	30064164	30070457	+
ACTR3	chr2	113890063	113962596	+
ACTR2	chr2	65227753	65271253	+
AL049629.2	chr11	33698261	33722467	-
ACOT9	chrX	23701055	23766475	-
AK3	chr9	4709556	4742043	-
ACAP1	chr17	7336529	7351477	+
AC008982.1	chr19	38817471	38840178	-
ADGRE1	chr19	6887566	6940459	+
AL669918.1	chr6	32813767	32838822	-
AC007192.1	chr19	18153158	18178117	+
ACTB	chr7	5527148	5563784	-
AL590764.2	chrX	71103987	71111575	-
AKR1B1	chr7	134442356	134459284	-
ALDH18A1	chr10	95605941	95656711	-
AC005670.2	chr17	46923133	47049932	+
AIP	chr11	67483026	67491103	+
AKR7A2	chr1	19303965	19312146	-
ACIN1	chr14	23058564	23095614	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-24-3p	chr9	95086064	95086085	+
hsa-miR-7-5p	chr19	4770700	4770723	+
hsa-miR-423-5p	chr17	30117095	30117117	+
hsa-miR-4687-3p	chr11	3856113	3856133	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC004687.1	chr17	58330884	58332508	-
AC007952.4	chr17	19112000	19112636	-
AC016876.2	chr17	7581964	7584086	-
AC020663.1	chr16	4730115	4752565	-
AL137802.2	chr1	16514645	16515754	+

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.