exRNAdisease

General Information

Database ID:

exR0000173

RNA Name:

ACSL4

RNA Type:

mRNA

Chromosome:

chrX

Starnd:

Coordinate:

Start Site(bp):

109624244

End Site(bp):

109733403

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
CEP78	chr9	78236062	78279690	+
RPL23	chr17	38847860	38853764	-
ADGRL1	chr19	14147743	14206187	-
LRBA	chr4	150264435	151015727	-
ACOT2	chr14	73567620	73575658	+
COX8A	chr11	63974620	63976543	+
PITPNC1	chr17	67377281	67697261	+
BEX5	chrX	102153708	102155977	-
NUDT21	chr16	56429133	56452199	-
NUCKS1	chr1	205712822	205750182	-
BHLHE40	chr3	4979437	4985323	+
ZMYM4	chr1	35268709	35422058	+
KCNE5	chrX	109623700	109625172	-
C9orf40	chr9	74946583	74952912	-
CPZ	chr4	8592660	8619759	+
MZT2A	chr2	131464900	131492743	-
ENO1	chr1	8861000	8879190	-
ARPC5	chr1	183620846	183635783	-
ZMAT2	chr5	140698680	140706686	+
MKNK2	chr19	2037465	2051244	-
MTRNR2L1	chr17	22523111	22524663	+
HELQ	chr4	83407343	83455855	-
GAPDH	chr12	6534512	6538374	+
FOXRED1	chr11	126269055	126278131	+
KRAS	chr12	25205246	25250936	-
TIMM17B	chrX	48893447	48898143	-
COPB2	chr3	139355600	139389680	-
UBL7	chr15	74445977	74461182	-
CDS2	chr20	5126879	5197887	+
EFTUD2	chr17	44849948	44899445	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-34a-5p	chr1	9151735	9151756	-
hsa-miR-34c-5p	chr11	111513451	111513473	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC106864.1	chr4	112693047	112706810	-
AL117378.1	chr6	131901963	131920565	+
AP003175.1	chr11	75069243	75096964	-
NEAT1	chr11	65422774	65445540	+
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.