exRNAdisease

General Information

Database ID:

exR0002308

RNA Name:

CCT7

RNA Type:

mRNA

Chromosome:

chr2

Starnd:

Coordinate:

Start Site(bp):

73233420

End Site(bp):

73253021

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
A1BG	chr19	58345178	58353492	-
ABHD16A	chr6	31686955	31703356	-
AC004832.3	chr22	30409255	30428990	+
AC010422.3	chr19	12643831	12648397	-
AC010463.1	chr19	17267418	17282966	+
AC011511.4	chr19	10315471	10320678	-
AC091167.2	chr15	90249556	90272208	+
AC092143.1	chr16	89919165	89936092	+
ACIN1	chr14	23058564	23095614	-
ACO1	chr9	32384603	32454769	+
ACOT7	chr1	6264269	6394391	-
ACTA2	chr10	88935074	88991339	-
ACTG1	chr17	81509971	81523847	-
ACTN4	chr19	38647649	38731589	+
ADA2	chr22	17178790	17258235	-
ADAMTS7	chr15	78759206	78811464	-
ADGRL1	chr19	14147743	14206187	-
ADI1	chr2	3497366	3519531	-
ADNP	chr20	50888916	50931437	-
AFMID	chr17	78187317	78207701	+
AGTRAP	chr1	11736084	11754802	+
AHCY	chr20	34280268	34311802	-
AIF1	chr6	31615217	31617021	+
AIF1L	chr9	131096476	131123152	+
AL136454.1	chr1	192716132	192716653	+
ALDH7A1	chr5	126531200	126595362	-
ALDOA	chr16	30064164	30070457	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-3654	chr7	133034860	133034878	-
hsa-miR-4426	chr1	192716333	192716349	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC012313.3	chr19	58346854	58362751	-
AC093904.4	chr2	9106593	9109865	+
AC133644.3	chr2	87455476	87767359	+
AC245014.3	chr1	145281116	145281462	+

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.