exRNAdisease

General Information

Database ID:

exR0015572

RNA Name:

TUBA1C

RNA Type:

mRNA

Chromosome:

chr12

Starnd:

Coordinate:

Start Site(bp):

49188736

End Site(bp):

49274603

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
ADCK2	chr7	140672945	140696261	+
AHCYL1	chr1	109984765	110023742	+
ALDH7A1	chr5	126531200	126595362	-
AC010323.1	chr19	8308283	8321379	-
AL139011.2	chr1	160216800	160285130	-
ADNP2	chr18	80109262	80147523	+
ABR	chr17	1003518	1229738	-
ABCA2	chr9	137007234	137028922	-
ACBD5	chr10	27195214	27242130	-
AC027644.4	chr7	66628958	66811189	+
AC093525.2	chr16	2496032	2520218	+
ACAT2	chr6	159762045	159779112	+
AK9	chr6	109492856	109691217	-
ADORA1	chr1	203090654	203167405	+
AHCY	chr20	34280268	34311802	-
ACTB	chr7	5527148	5563784	-
AGTRAP	chr1	11736084	11754802	+
ACIN1	chr14	23058564	23095614	-
ACTR3	chr2	113890063	113962596	+
AGBL3	chr7	134986508	135147963	+
ACTG1	chr17	81509971	81523847	-
AGK	chr7	141551278	141655244	+
ACTL6A	chr3	179562886	179588407	+
AC008982.1	chr19	38817471	38840178	-
AL162231.3	chr9	34646645	34657113	+
ALDOA	chr16	30064164	30070457	+
AL136454.1	chr1	192716132	192716653	+
AC004922.1	chr7	99325879	99394653	+
AC092143.1	chr16	89919165	89936092	+
ACTR1B	chr2	97655939	97664044	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-367-3p	chr4	112647877	112647898	-
hsa-miR-3610	chr8	116874740	116874759	-
hsa-miR-3654	chr7	133034860	133034878	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC004687.1	chr17	58330884	58332508	-
AC011298.1	chr2	240686334	240690414	+
AC026362.1	chr12	122975320	122982907	+
AC233266.2	chr2	91580336	91580863	+

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.