exRNAdisease

General Information

Database ID:

exR0000140

RNA Name:

ACKR3

RNA Type:

mRNA

Chromosome:

chr2

Starnd:

Coordinate:

Start Site(bp):

236567787

End Site(bp):

236582354

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
CBSL	chr21	6444869	6468040	-
EIF3C	chr16	28688558	28735730	+
TOP2B	chr3	25597905	25664907	-
HNRNPH2	chrX	101408222	101414133	+
EXOC8	chr1	231332753	231337852	-
TMEM106B	chr7	12211270	12243367	+
AHCY	chr20	34280268	34311802	-
PKM	chr15	72199029	72231822	-
HMGB2	chr4	173331376	173334432	-
SPTAN1	chr9	128552558	128633662	+
ADK	chr10	74151202	74709963	+
AKAP1	chr17	57085092	57121346	+
LIN28A	chr1	26410817	26429728	+
RPL13A	chr19	49487554	49492308	+
CTNND1	chr11	57753243	57819546	+
ZNF318	chr6	43307134	43369647	-
CCT4	chr2	61868085	61888671	-
PRICKLE3	chrX	49174802	49186528	-
WDR83OS	chr19	12668073	12669415	-
ARNT	chr1	150809713	150876708	-
EZR	chr6	158765741	158819368	-
CBS	chr21	43053191	43076943	-
HEY2	chr6	125747664	125761269	+
PHC2	chr1	33323623	33431052	-
RIBC2	chr22	45413693	45432509	+
HLA-DRB5	chr6	32517353	32530287	-
NAP1L1	chr12	76036585	76084958	-
HNRNPA1	chr12	54280193	54287088	+
EIF4A3	chr17	80134369	80147151	-
CLSTN1	chr1	9728926	9823984	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-455-3p	chr9	114209487	114209507	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC007743.1	chr2	56173534	56185870	-
AC132217.1	chr11	2129121	2129964	-

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.