exRNAdisease

General Information

Database ID:

exR0000109

RNA Name:

ACACA

RNA Type:

mRNA

Chromosome:

chr17

Starnd:

Coordinate:

Start Site(bp):

37084992

End Site(bp):

37406836

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
XPNPEP3	chr22	40857077	40932815	+
SORT1	chr1	109309568	109397918	-
LSM2	chr6	31797396	31806966	-
RB1CC1	chr8	52622458	52745843	-
ATXN1L	chr16	71845976	71885268	+
EIF3F	chr11	7970251	8001862	+
RPL10A	chr6	35468401	35470785	+
RAB40B	chr17	82654973	82698698	-
GANAB	chr11	62624826	62646726	-
NPC2	chr14	74476192	74494177	-
PMAIP1	chr18	59899948	59904306	+
TCF19	chr6	31158547	31167159	+
ATP2A2	chr12	110280756	110351093	+
METTL9	chr16	21597218	21657473	+
KMT2D	chr12	49018975	49059774	-
GAPDH	chr12	6534512	6538374	+
TLE3	chr15	70047790	70098176	-
SEPHS1	chr10	13317428	13348298	-
AC079447.1	chr2	99141485	99322741	+
FBXW11	chr5	171861549	172006873	-
FBRS	chr16	30658431	30670810	+
FAM126A	chr7	22889371	23014130	-
IQGAP1	chr15	90388242	90502239	+
CACHD1	chr1	64470129	64693058	+
PDE8A	chr15	84980440	85139145	+
DVL1	chr1	1335276	1349418	-
SIMC1	chr5	176238367	176345991	+
MRPL57	chr13	21176658	21179084	+
MTRNR2L8	chr11	10507894	10509186	-
DDX6	chr11	118747763	118791164	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-541-3p	chr14	101064548	101064569	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC008514.1	chr5	170747047	170788650	-
AD000090.1	chr19	35557956	35581954	+
AC079601.2	chr12	42459366	42466128	+
AC138761.1	chr17	22266395	22288301	+
AP001496.2	chr18	5232876	5238526	-
MIR663AHG	chr20	26167817	26251546	-
MMP25-AS1	chr16	3037400	3059370	-
RMRP	chr9	35657751	35658018	-
RMST	chr12	97430884	97598415	+
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.