exRNAdisease

General Information

Database ID:

exR0006887

RNA Name:

ILF3

RNA Type:

mRNA

Chromosome:

chr19

Starnd:

Coordinate:

Start Site(bp):

10654261

End Site(bp):

10692417

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
AC010422.3	chr19	12643831	12648397	-
AGO1	chr1	35869808	35930532	+
AC093525.2	chr16	2496032	2520218	+
AC105052.3	chr7	102637049	102671641	-
AC105052.1	chr7	102582523	102642869	-
ACY1	chr3	51983340	51989197	+
ADH5	chr4	99070978	99088801	-
ADARB1	chr21	45073853	45226560	+
ACTL6A	chr3	179562886	179588407	+
AGPAT2	chr9	136673143	136687457	-
AC005258.1	chr19	2269525	2341172	+
ALDOA	chr16	30064164	30070457	+
ABCA7	chr19	1039997	1065572	+
AASS	chr7	122073549	122144255	-
ABHD14A-ACY1	chr3	51974706	51989183	+
AL035078.4	chr11	31812391	32104665	+
ACOT7	chr1	6264269	6394391	-
AEN	chr15	88621337	88632281	+
AKR1A1	chr1	45550543	45570049	+
AGAP1	chr2	235494043	236131800	+
AL590132.1	chr1	210858125	211134146	-
ABCF1	chr6	30571393	30597179	+
AC011462.1	chr19	41350853	41425001	+
AC027796.3	chr17	3585149	3636249	-
ACTG1	chr17	81509971	81523847	-
AC124312.1	chr15	24955034	25000276	+
ACTB	chr7	5527148	5563784	-
AL031708.1	chr16	1632259	1686715	+
ACBD6	chr1	180269653	180502954	-
ABHD14B	chr3	51968510	51983409	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-147a	chr9	120244985	120245004	-
hsa-miR-27b-3p	chr9	95085505	95085525	+
hsa-miR-513a-5p	chrX	147213538	147213555	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC010536.1	chr16	87693537	87696147	-
AC125807.2	chr12	3041437	3044950	+
AC132217.1	chr11	2129121	2129964	-
AC139149.1	chr17	81514047	81527776	+
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.