exRNAdisease

General Information

Database ID:

exR0005171

RNA Name:

FGFR1

RNA Type:

mRNA

Chromosome:

chr8

Starnd:

Coordinate:

Start Site(bp):

38400215

End Site(bp):

38468834

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
ABCC4	chr13	95019835	95301475	-
ABCF1	chr6	30571393	30597179	+
ABHD17A	chr19	1876810	1885547	-
ABI2	chr2	203328239	203447728	+
AC002996.1	chr12	111753890	111791418	+
AC005258.1	chr19	2269525	2341172	+
AC067968.1	chr19	44025354	44087318	+
AC107871.1	chr15	68184032	68229718	-
AC139530.2	chr17	81703371	81720539	+
ACACA	chr17	37084992	37406836	-
ACAD10	chr12	111686056	111757107	+
ACLY	chr17	41866917	41930542	-
ACOT7	chr1	6264269	6394391	-
ACTB	chr7	5527148	5563784	-
ACTG1	chr17	81509971	81523847	-
AGAP1	chr2	235494043	236131800	+
AGPAT5	chr8	6708642	6761503	+
AKIRIN1	chr1	38991276	39006059	+
AKR1E2	chr10	4786629	4848062	+
AL121845.3	chr20	63708864	63739103	+
AL589666.1	chr6	85557978	85615234	-
ALDH4A1	chr1	18871430	18902724	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-214-3p	chr1	172138816	172138837	-
hsa-miR-184	chr15	79209840	79209861	+
hsa-miR-195-5p	chr17	7017667	7017687	-
hsa-miR-543	chr14	101032033	101032054	+
hsa-miR-1286	chr22	20249145	20249165	-
hsa-miR-1294	chr5	154347153	154347174	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC022167.2	chr16	8848105	8860456	+
AL022311.1	chr22	37876148	37895563	+

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.