exRNAdisease

General Information

Database ID:

exR0000182

RNA Name:

ACSS2

RNA Type:

mRNA

Chromosome:

chr20

Starnd:

Coordinate:

Start Site(bp):

34872146

End Site(bp):

34927962

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
RPS19	chr19	41860255	41872925	+
TUBA1B	chr12	49127782	49131397	-
VPS26B	chr11	134224671	134247788	+
EIF6	chr20	35278911	35284985	-
KIAA0930	chr22	45190338	45240769	-
KLHDC4	chr16	87696485	87765992	-
TXNL4A	chr18	79970813	80033949	-
TUBA1A	chr12	49184795	49189080	-
NDUFB1	chr14	92116122	92121917	-
DUT	chr15	48331011	48343373	+
NUCKS1	chr1	205712822	205750182	-
SIK3	chr11	116843402	117098437	-
COPS7B	chr2	231781671	231809254	+
LMBR1	chr7	156668946	156893216	-
PFN1	chr17	4945652	4949061	-
SLC52A3	chr20	760080	776015	-
BLOC1S4	chr4	6716174	6717664	+
GDI2	chr10	5765223	5842132	-
DDX5	chr17	64498254	64508199	-
TPI1	chr12	6867119	6870948	+
KXD1	chr19	18557762	18569387	+
NDUFS7	chr19	1383527	1395589	+
DPF2	chr11	65333852	65354262	+
AL121753.1	chr20	35267885	35280043	-
STAT5B	chr17	42199177	42276707	-
RPS11	chr19	49496365	49499708	+
DYNLL1	chr12	120469850	120498493	+
PPP6R1	chr19	55229779	55259017	-
STAU1	chr20	49113339	49188367	-
HSP90AB1	chr6	44246166	44253888	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-18a-5p	chr13	91350756	91350778	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AL022311.1	chr22	37876148	37895563	+
AL022332.1	chr22	25279529	25282674	-
GAS5	chr1	173858559	173868882	-
LINC01405	chr12	110934590	110959093	+
MIR17HG	chr13	91347820	91354579	+

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.