exRNAdisease

General Information

Database ID:

exR0005221

RNA Name:

FKBP8

RNA Type:

mRNA

Chromosome:

chr19

Starnd:

Coordinate:

Start Site(bp):

18531751

End Site(bp):

18544077

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
ABCA5	chr17	69244311	69327244	-
ABCC4	chr13	95019835	95301475	-
ABR	chr17	1003518	1229738	-
AC007192.1	chr19	18153158	18178117	+
AC008878.3	chr19	7382834	7470241	+
AC010132.3	chr7	42909273	42932174	-
AC012184.2	chr16	70299194	70372582	+
AC024592.3	chr19	5866171	5903787	-
AC055811.2	chr17	17202649	17237185	-
AC073896.1	chr12	56285916	56316059	-
AC138811.2	chr16	18788063	18801519	-
ACAT2	chr6	159762045	159779112	+
ACTB	chr7	5527148	5563784	-
ACTG1	chr17	81509971	81523847	-
ACTR1A	chr10	102461881	102502712	-
ADCK5	chr8	144373101	144393242	+
ADGRE2	chr19	14732392	14778560	-
ADGRL1	chr19	14147743	14206187	-
ADO	chr10	62804720	62808479	+
AEN	chr15	88621337	88632281	+
AFDN	chr6	167826922	167972023	+
AGPAT3	chr21	43865223	43987592	+
AHCTF1	chr1	246839098	246931967	-
AIFM1	chrX	130129362	130165887	-
AKAP10	chr17	19904302	19978343	-
AKNA	chr9	114334156	114394405	-
AL365205.1	chr6	41780349	41790141	+
AL603832.3	chr1	112702614	112711433	-
ALCAM	chr3	105366909	105576900	+
ALDOA	chr16	30064164	30070457	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-3652	chr12	103930425	103930442	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC005899.4	chr17	32328441	32329395	+
AC010615.2	chr19	21444241	21463908	-
AC026362.1	chr12	122975320	122982907	+
AC069281.2	chr7	100572232	100578700	-
AC074183.1	chr7	84939349	84940245	-
AC099778.1	chr3	47379089	47380999	-
AC106864.1	chr4	112693047	112706810	-
AC109460.3	chr16	28974804	28990775	+
AC113189.2	chr17	7420103	7444081	+
AC113189.4	chr17	7439506	7445966	+
AC245014.3	chr1	145281116	145281462	+

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.