exRNAdisease

General Information

Database ID:

exR0000030

RNA Name:

ABCA3

RNA Type:

mRNA

Chromosome:

chr16

Starnd:

Coordinate:

Start Site(bp):

2275881

End Site(bp):

2340746

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
ATG2B	chr14	96279195	96363341	-
BCAR1	chr16	75228181	75268053	-
LAMB2	chr3	49121114	49133118	-
HLA-F	chr6	29722775	29738528	+
NOC4L	chr12	132144457	132152473	+
HS3ST3A1	chr17	13494032	13601929	-
ASRGL1	chr11	62337448	62393412	+
HNRNPUL2-BSCL2	chr11	62690275	62727384	-
SIK3	chr11	116843402	117098437	-
MCMBP	chr10	119829404	119892556	-
CYB5R3	chr22	42617840	42649392	-
RPL11	chr1	23691742	23696835	+
KLHL21	chr1	6590724	6614607	-
PVRIG	chr7	100218241	100221490	+
ZNF219	chr14	21090077	21104722	-
PKM	chr15	72199029	72231822	-
HMGB2	chr4	173331376	173334432	-
DNAJC18	chr5	139408588	139444491	-
MT-ND4L	chrMT	10470	10766	+
CHTF18	chr16	788046	800737	+
CDH4	chr20	61252261	61940617	+
TSC2	chr16	2047967	2089491	+
CDCA2	chr8	25459199	25507911	+
TPRN	chr9	137191617	137204193	-
HLA-E	chr6	30489509	30494194	+
DCP2	chr5	112976702	113022195	+
FAM104A	chr17	73207353	73236753	-
BUB3	chr10	123154402	123170467	+
RFWD3	chr16	74621399	74666877	-
TUBB2A	chr6	3153666	3157544	-

miRNA targets:

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC022167.2	chr16	8848105	8860456	+
AC245014.3	chr1	145281116	145281462	+
XIST	chrX	73820649	73852723	-

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.