exRNAdisease

General Information

Database ID:

exR0014091

RNA Name:

STMN1

RNA Type:

mRNA

Chromosome:

chr1

Starnd:

Coordinate:

Start Site(bp):

25884181

End Site(bp):

25906991

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
AAMP	chr2	218264123	218270257	-
ABCE1	chr4	145098288	145129524	+
ABHD16A	chr6	31686955	31703356	-
ABI2	chr2	203328239	203447728	+
AC007192.1	chr19	18153158	18178117	+
AC118549.1	chr1	77562416	77683419	-
AC138811.2	chr16	18788063	18801519	-
ACOT9	chrX	23701055	23766475	-
ACTB	chr7	5527148	5563784	-
ACTG1	chr17	81509971	81523847	-
ACTN4	chr19	38647649	38731589	+
ACTR1B	chr2	97655939	97664044	-
ACTR5	chr20	38748460	38772520	+
AD000671.1	chr19	35745678	35754519	+
ADAM19	chr5	157395534	157575775	-
ADK	chr10	74151202	74709963	+
AGPS	chr2	177392757	177559299	+
AL117348.2	chr1	225886696	225924278	-
AL136295.1	chr14	24189157	24213473	-
AL136295.4	chr14	24180395	24190416	-
ALDH7A1	chr5	126531200	126595362	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-194-5p	chr11	64891404	64891425	-
hsa-miR-3654	chr7	133034860	133034878	-
hsa-miR-3917	chr1	25906384	25906403	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC005618.1	chr5	141326210	141329357	+
AC006504.5	chr19	27793431	27984984	+
AC023509.1	chr12	53441741	53467528	+
AC106864.1	chr4	112693047	112706810	-
AC132217.1	chr11	2129121	2129964	-

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.