exRNAdisease

General Information

Database ID:

exR0000183

RNA Name:

ACSS3

RNA Type:

mRNA

Chromosome:

chr12

Starnd:

Coordinate:

Start Site(bp):

80936414

End Site(bp):

81261210

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
TRAM1L1	chr4	117083554	117085576	-
NMNAT2	chr1	183248237	183418380	-
EPB41L2	chr6	130839347	131063322	-
CNST	chr1	246566444	246668595	+
TJP1	chr15	29699367	29968865	-
UBL7	chr15	74445977	74461182	-
SENP3-EIF4A1	chr17	7563287	7578715	+
UBE2E1	chr3	23805955	23891640	+
MIDN	chr19	1248553	1259140	+
TUBB	chr6	30720352	30725426	+
KXD1	chr19	18557762	18569387	+
U2SURP	chr3	142964497	143060725	+
TPI1	chr12	6867119	6870948	+
UBE2D2	chr5	139526431	139628434	+
SCAPER	chr15	76347904	76905444	-
PTGES3	chr12	56663341	56688408	-
DEK	chr6	18223860	18264548	-
OPRD1	chr1	28812142	28871267	+
POLR1D	chr13	27620742	27744237	+
RPS23	chr5	82273320	82278396	-
EIF4A1	chr17	7572706	7579006	+
RHEB	chr7	151466012	151520120	-
RPS6KC1	chr1	213051233	213274774	+
ME2	chr18	50879080	50954257	+
ARF4	chr3	57571363	57598220	-
ENO1	chr1	8861000	8879190	-
SWT1	chr1	185157080	185291781	+
CRABP2	chr1	156699606	156705816	-
NONO	chrX	71283192	71301168	+
HMGN4	chr6	26538366	26546933	+

miRNA targets:

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC016876.2	chr17	7581964	7584086	-
NIFK-AS1	chr2	121649320	121728563	+

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.