exRNAdisease

General Information

Database ID:

exR0000451

RNA Name:

AKIRIN1

RNA Type:

mRNA

Chromosome:

chr1

Starnd:

Coordinate:

Start Site(bp):

38991276

End Site(bp):

39006059

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
CHIC2	chr4	54009789	54064605	-
NOP10	chr15	34341713	34343177	-
DDX54	chr12	113157174	113185479	-
RBM39	chr20	35701347	35742312	-
MCFD2	chr2	46901870	46941855	-
KIAA0319L	chr1	35433492	35557950	-
SH2B3	chr12	111405923	111451623	+
IST1	chr16	71845996	71931199	+
KMT5C	chr19	55339853	55348121	+
CCNB1IP1	chr14	20311368	20333312	-
PJA2	chr5	109334713	109409974	-
DNAJB9	chr7	108569867	108574850	+
RAB3B	chr1	51907956	51990700	-
ANKRD17	chr4	73073376	73258798	-
EIF3B	chr7	2354086	2380745	+
PPP1CC	chr12	110719680	110742939	-
SLC38A1	chr12	46183063	46270017	-
CTSD	chr11	1752755	1764573	-
EIF4H	chr7	74174245	74197101	+
C12orf65	chr12	123233436	123257960	+
TFRC	chr3	196027183	196082096	-
TXNDC5	chr6	7881517	7910788	-
G3BP1	chr5	151771045	151812785	+
EP400	chr12	131949942	132080460	+
ZFC3H1	chr12	71609472	71667725	-
TKT	chr3	53224712	53256052	-
CKS2	chr9	89311195	89316703	+
TXN	chr9	110243810	110256507	-
EPAS1	chr2	46293667	46386697	+
ASB1	chr2	238426742	238452250	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-367-3p	chr4	112647877	112647898	-
hsa-miR-1321	chrX	85835832	85835849	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC138761.1	chr17	22266395	22288301	+
AP001496.2	chr18	5232876	5238526	-
ARSD-AS1	chrX	2904904	2906081	+
LINC01783	chr1	16533886	16536172	-
MAPKAPK5-AS1	chr12	111839764	111842902	-
SCARNA9	chr11	93721513	93721865	+
SNHG5	chr6	85650491	85678932	-

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.