exRNAdisease

General Information

Database ID:

exR0001953

RNA Name:

CALR

RNA Type:

mRNA

Chromosome:

chr19

Starnd:

Coordinate:

Start Site(bp):

12938578

End Site(bp):

12944489

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
AARSD1	chr17	42950526	42964498	-
ABCF2	chr7	151207837	151227166	-
ABHD14B	chr3	51968510	51983409	-
ABI1	chr10	26746593	26861087	-
ABRACL	chr6	139028745	139043302	+
AC005943.1	chr19	1578339	1605445	-
AC007192.1	chr19	18153158	18178117	+
AC069503.2	chr12	121888809	121921470	+
AC138811.2	chr16	18788063	18801519	-
ACAD8	chr11	134253495	134265855	+
ACTB	chr7	5527148	5563784	-
ACTG1	chr17	81509971	81523847	-
ACTR1A	chr10	102461881	102502712	-
ACTR3	chr2	113890063	113962596	+
ADCYAP1R1	chr7	31052461	31111479	+
ADNP2	chr18	80109262	80147523	+
AHCY	chr20	34280268	34311802	-
AK3	chr9	4709556	4742043	-
AKAP8	chr19	15353385	15379798	-
AKT2	chr19	40230317	40285536	-
ALDOA	chr16	30064164	30070457	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-663a	chr20	26208243	26208264	-
hsa-miR-423-5p	chr17	30117095	30117117	+
hsa-miR-541-3p	chr14	101064548	101064569	+
hsa-miR-6515-5p	chr19	12940486	12940506	+
hsa-miR-6515-3p	chr19	12940521	12940540	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC012236.1	chr15	31221999	31230838	-
AC026362.1	chr12	122975320	122982907	+
AC064802.1	chr8	114282067	114295839	+
AC132217.1	chr11	2129121	2129964	-
AD000090.1	chr19	35557956	35581954	+
AL021707.1	chr22	38739003	38749041	+

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.