exRNAdisease

General Information

Database ID:

exR0000490

RNA Name:

ALDH5A1

RNA Type:

mRNA

Chromosome:

chr6

Starnd:

Coordinate:

Start Site(bp):

24494867

End Site(bp):

24537207

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
YWHAB	chr20	44885702	44908532	+
B2M	chr15	44711487	44718877	+
SLC25A6	chrX	1386152	1392113	-
MAP7D1	chr1	36155579	36180849	+
TTC19	chr17	15999784	16045015	+
EIF3E	chr8	108201216	108435333	-
FBRSL1	chr12	132489551	132585188	+
IRF2BP2	chr1	234604269	234609525	-
USP53	chr4	119212587	119295517	+
SH3GLB2	chr9	129007036	129028303	-
MYO10	chr5	16661907	16936288	-
TET3	chr2	73986404	74108176	+
STK11IP	chr2	219597857	219616451	+
NFKB2	chr10	102394110	102402524	+
MAPK12	chr22	50245450	50261716	-
ERRFI1	chr1	8004404	8026309	-
PNMA2	chr8	26504701	26514092	-
HUWE1	chrX	53532096	53686728	-
GTF2F1	chr19	6379572	6393981	-
RPS6	chr9	19375715	19380236	-
RPL37A	chr2	216498825	216579180	+
SLX1A	chr16	30193887	30197561	+
BAX	chr19	48954815	48961798	+
IGF2	chr11	2129112	2141238	-
KLC4	chr6	43040777	43075095	+
ZNF33A	chr10	38010650	38065088	+
ZNF12	chr7	6688433	6706947	-
LASP1	chr17	38869859	38921770	+
RPL13	chr16	89560657	89566828	+
FAM104B	chrX	55143102	55161310	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-129-5p	chr7	128207876	128207896	+
hsa-miR-330-5p	chr19	45639049	45639070	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC022201.2	chr2	70301451	70302072	+
AL645941.1	chr6	32970232	32970886	+

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.