exRNAdisease

General Information

Database ID:

exR0000092

RNA Name:

ABI2

RNA Type:

mRNA

Chromosome:

chr2

Starnd:

Coordinate:

Start Site(bp):

203328239

End Site(bp):

203447728

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
C15orf39	chr15	75195643	75212169	+
KLC1	chr14	103561896	103714249	+
PGAM1	chr10	97426191	97433444	+
ESPL1	chr12	53268299	53293638	+
COX5B	chr2	97646062	97648383	+
MYH9	chr22	36281277	36388067	-
YWHAQ	chr2	9583967	9630997	-
HLA-DQA1	chr6	32628179	32647062	+
MAN1B1	chr9	137086985	137109183	+
PUDP	chrX	6667865	7148190	-
PEX19	chr1	160276812	160286348	-
PKM	chr15	72199029	72231822	-
TRAF7	chr16	2155698	2178129	+
DICER1	chr14	95086228	95158010	-
LAMTOR4	chr7	100148907	100155944	+
ATN1	chr12	6924463	6942321	+
LMNB1	chr5	126776623	126837020	+
AL139300.1	chr14	103562962	103685924	+
SLC15A4	chr12	128793194	128823958	-
CCT2	chr12	69585426	69601570	+
NPLOC4	chr17	81556887	81648465	-
MT-CO3	chrMT	9207	9990	+
SLC9A3R1	chr17	74748628	74769353	+
API5	chr11	43311963	43344529	+
HSDL2	chr9	112380080	112472405	+
BOLA2-SMG1P6	chr16	29443230	29454651	-
TXNDC5	chr6	7881517	7910788	-
C9orf40	chr9	74946583	74952912	-
RPL22L1	chr3	170864875	170870208	-
HYOU1	chr11	119044188	119057227	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-218-5p	chr5	168768211	168768231	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC079354.2	chr2	202178660	202179391	-
ARHGAP27P1-BPTFP1-KPNA2P3	chr17	64749663	64781707	-

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.