exRNAdisease

General Information

Database ID:

exR0000426

RNA Name:

AK1

RNA Type:

mRNA

Chromosome:

chr9

Starnd:

Coordinate:

Start Site(bp):

127866486

End Site(bp):

127877675

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
ABHD17C	chr15	80679684	80755621	+
BCL11B	chr14	99169287	99272197	-
C9orf16	chr9	128160265	128163924	+
CBR3	chr21	36135079	36146562	+
CBX5	chr12	54230942	54280133	-
CLASP1	chr2	121337776	121649587	-
DBNDD1	chr16	90004871	90020128	-
ECI1	chr16	2239402	2252300	-
EIF4A1	chr17	7572706	7579006	+
HNRNPA1P48	chr16	51553436	51647132	+
HNRNPA3	chr2	177212563	177223958	+
IGFBP2	chr2	216632828	216664436	+
KANK1	chr9	470291	746106	+
LCMT1	chr16	25111731	25178231	+
MANEAL	chr1	37793802	37801137	+
MBNL1	chr3	152243828	152465780	+
NIP7	chr16	69337996	69343106	+
PRCP	chr11	82822936	82970584	-
RPS12	chr6	132814569	132817564	+
RPS19	chr19	41860255	41872925	+
SAP30L	chr5	154445997	154461053	+
SENP3-EIF4A1	chr17	7563287	7578715	+
SLC44A2	chr19	10602457	10644557	+
SYNRG	chr17	37514807	37609472	-
TBCEL	chr11	121024072	121090775	+
YTHDF2	chr1	28736621	28769775	+

miRNA targets:

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC016876.2	chr17	7581964	7584086	-
AL157935.2	chr9	127934503	127940952	+
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.