exRNAdisease

General Information

Database ID:

exR0001981

RNA Name:

CANX

RNA Type:

mRNA

Chromosome:

chr5

Starnd:

Coordinate:

Start Site(bp):

179678628

End Site(bp):

179731641

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
AACS	chr12	125065434	125143333	+
AAR2	chr20	36236459	36270918	+
AC005837.2	chr17	76732978	76738522	+
AC009133.6	chr16	29812261	29820092	+
AC010463.1	chr19	17267418	17282966	+
AC011511.4	chr19	10315471	10320678	-
AC078927.1	chr12	66123917	66169985	-
AC093323.1	chr4	6663396	6676755	+
AC131160.1	chr3	183815568	183884889	-
ACADVL	chr17	7217125	7225266	+
ACKR3	chr2	236567787	236582354	+
ACOT8	chr20	45841721	45857405	-
ACTG1	chr17	81509971	81523847	-
ACVR2B	chr3	38453890	38493142	+
ADAM9	chr8	38996869	39105261	+
ADAMTS1	chr21	26835755	26845409	-
ADGRA3	chr4	22345071	22516066	-
ADGRV1	chr5	90529344	91164437	+
ADH5	chr4	99070978	99088801	-
ADNP	chr20	50888916	50931437	-
AGO1	chr1	35869808	35930532	+
AGPAT1	chr6	32168212	32178096	-
AGPS	chr2	177392757	177559299	+
AIMP1	chr4	106315544	106349456	+
AKAP10	chr17	19904302	19978343	-
AKAP11	chr13	42272152	42323261	+
AKAP8L	chr19	15380050	15419141	-
AL589666.1	chr6	85557978	85615234	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-27a-3p	chr19	13836447	13836467	-
hsa-miR-27b-3p	chr9	95085505	95085525	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC005618.1	chr5	141326210	141329357	+
AC012321.1	chr16	69703065	69704652	+
AC023509.1	chr12	53441741	53467528	+
AC107068.1	chr4	47840122	47844339	-
AC127459.1	chr16	23061406	23064173	-
AL118506.1	chr20	63861212	63864293	-
AL139089.1	chr13	52651305	52652279	-

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.