exRNAdisease

General Information

Database ID:

exR0001947

RNA Name:

CALM3

RNA Type:

mRNA

Chromosome:

chr19

Starnd:

Coordinate:

Start Site(bp):

46601074

End Site(bp):

46610782

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
ALDH6A1	chr14	74056847	74084492	-
ADAMTSL4	chr1	150549369	150560937	+
ABHD12	chr20	25294742	25390835	-
AGPAT1	chr6	32168212	32178096	-
ACOT13	chr6	24667035	24705065	+
AHCY	chr20	34280268	34311802	-
AGO1	chr1	35869808	35930532	+
ALDH7A1	chr5	126531200	126595362	-
AAMDC	chr11	77821109	77918432	+
ADAR	chr1	154582057	154628013	-
AHSA1	chr14	77457870	77469472	+
AC006486.1	chr19	42234583	42255132	-
AC010422.3	chr19	12643831	12648397	-
ABI2	chr2	203328239	203447728	+
AL121594.1	chr14	35122549	35317474	+
ALDH18A1	chr10	95605941	95656711	-
AC099811.2	chr17	42119674	42154916	-
ABCC5	chr3	183919934	184017939	-
ACTG1	chr17	81509971	81523847	-
AIF1L	chr9	131096476	131123152	+
AC245033.1	chr15	82536788	82573194	-
ACACA	chr17	37084992	37406836	-
ADAM19	chr5	157395534	157575775	-
ABTB1	chr3	127672935	127680926	+
ACTB	chr7	5527148	5563784	-
ACIN1	chr14	23058564	23095614	-
AGAP1	chr2	235494043	236131800	+
AC009133.6	chr16	29812261	29820092	+
AARSD1	chr17	42950526	42964498	-
AC090360.1	chr18	80034346	80097088	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-34a-5p	chr1	9151735	9151756	-
hsa-miR-205-5p	chr1	209432166	209432187	+
hsa-miR-449a	chr5	55170586	55170607	-
hsa-miR-449b-5p	chr5	55170706	55170727	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC016876.2	chr17	7581964	7584086	-
AC026362.1	chr12	122975320	122982907	+
AC079781.5	chr7	97851688	97972985	-
AC093503.2	chr19	46609277	46610779	-
AC125807.2	chr12	3041437	3044950	+
AD000090.1	chr19	35557956	35581954	+
AL022311.1	chr22	37876148	37895563	+

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.