exRNAdisease

General Information

Database ID:

exR0006756

RNA Name:

IGF2

RNA Type:

mRNA

Chromosome:

chr11

Starnd:

Coordinate:

Start Site(bp):

2129112

End Site(bp):

2141238

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
AL160269.1	chr9	96235331	96352058	-
AC120057.2	chr17	7240427	7244635	-
ADAMTSL4	chr1	150549369	150560937	+
ADK	chr10	74151202	74709963	+
ADAR	chr1	154582057	154628013	-
ADAMTS9	chr3	64515654	64688000	-
ACTR1B	chr2	97655939	97664044	-
ADSL	chr22	40346500	40390463	+
AL133352.1	chr10	100505628	100529881	-
AL121845.3	chr20	63708864	63739103	+
ADCY6	chr12	48766194	48789037	-
AIF1L	chr9	131096476	131123152	+
ADRM1	chr20	62302093	62308862	+
AKAP1	chr17	57085092	57121346	+
AC009133.6	chr16	29812261	29820092	+
AL360181.3	chr10	133380017	133420271	+
AC068547.1	chr2	151802651	151973949	-
ACIN1	chr14	23058564	23095614	-
ADAM8	chr10	133262420	133276868	-
ALDH16A1	chr19	49453225	49471050	+
ACTG1	chr17	81509971	81523847	-
AGPAT4	chr6	161129967	161274061	-
ADCK2	chr7	140672945	140696261	+
ACKR3	chr2	236567787	236582354	+
ADAMTS2	chr5	179110853	179345461	-
ADGRG6	chr6	142301854	142446266	+
AL022238.4	chr22	40346529	40410054	+
ADAT1	chr16	75596981	75623300	-
ACTR1A	chr10	102461881	102502712	-
AKIRIN1	chr1	38991276	39006059	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-147a	chr9	120244985	120245004	-
hsa-miR-218-5p	chr5	168768211	168768231	-
hsa-miR-147b-3p	chr15	45433098	45433118	+
hsa-miR-3609	chr7	98881700	98881723	+
hsa-miR-4442	chr3	25664875	25664891	-
hsa-miR-4485-3p	chr11	10508277	10508296	-
hsa-miR-6501-5p	chr21	33550664	33550685	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC002467.1	chr7	107739999	107744581	-
AC005562.1	chr17	30576464	30672789	+
AC007952.4	chr17	19112000	19112636	-
AC010327.5	chr19	55216660	55221616	+
AC016876.2	chr17	7581964	7584086	-
AC020928.2	chr19	36773712	36775908	-
AC022167.2	chr16	8848105	8860456	+
AC083964.1	chr8	450714	451343	-
AC095057.3	chr4	40166675	40167831	+
AC118758.3	chr7	56809214	56848800	-
AC132217.1	chr11	2129121	2129964	-
AC245014.3	chr1	145281116	145281462	+
AC245033.4	chr15	82533175	82540008	-
AD000090.1	chr19	35557956	35581954	+

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.