exRNAdisease

General Information

Database ID:

exR0000410

RNA Name:

AICDA

RNA Type:

mRNA

Chromosome:

chr12

Starnd:

Coordinate:

Start Site(bp):

8602170

End Site(bp):

8612867

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
ERCC5	chr13	102807146	102876001	+
UBE2Z	chr17	48908407	48929056	+
TAPBP	chr6	33299694	33314387	-
ALDH9A1	chr1	165662216	165698863	-
ITM2C	chr2	230864639	230879248	+
ACTR1B	chr2	97655939	97664044	-
LGMN	chr14	92703807	92748679	-
ABL1	chr9	130713016	130887675	+
AC027644.4	chr7	66628958	66811189	+
RPL30	chr8	98024851	98046469	-
ATP5MG	chr11	118401606	118431496	+
POMT2	chr14	77274956	77320884	-
RPS16	chr19	39433137	39435949	-
SMUG1	chr12	54121277	54189008	-
UBA2	chr19	34428352	34471251	+
DCAF1	chr3	51395867	51500002	-
MT-ND4	chrMT	10760	12137	+
NADSYN1	chr11	71453109	71524107	+
AP001781.2	chr11	111786286	111879425	-
GAPDH	chr12	6534512	6538374	+
NACA2	chr17	61590421	61591219	-
TOP2A	chr17	40388525	40417896	-
GAS2L3	chr12	100573683	100628288	+
POLG2	chr17	64477785	64497054	-
ATP5F1C	chr10	7788147	7807815	+
RPL8	chr8	144789765	144792587	-
MTRNR2L8	chr11	10507894	10509186	-
OVOL1	chr11	65787063	65797214	+
RABGEF1	chr7	66682164	66811464	+
SLC25A3	chr12	98593591	98606379	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-155-5p	chr21	25573983	25574006	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
LINC02154	chrX	13266048	13303452	-
MIR155HG	chr21	25561909	25575168	+
TSPOAP1-AS1	chr17	58324472	58415766	+

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.