exRNAdisease

General Information

Database ID:

exR0000486

RNA Name:

ALDH3A2

RNA Type:

mRNA

Chromosome:

chr17

Starnd:

Coordinate:

Start Site(bp):

19648136

End Site(bp):

19685760

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
BLM	chr15	90717346	90816166	+
C4orf3	chr4	119296419	119304445	-
KMT2D	chr12	49018975	49059774	-
EIF5A	chr17	7306999	7312463	+
PRSS16	chr6	27247701	27256624	+
NPM1	chr5	171387116	171411137	+
ERGIC3	chr20	35542021	35557634	+
BST2	chr19	17402939	17405630	-
IQGAP1	chr15	90388242	90502239	+
HMGCR	chr5	75336329	75362101	+
MTRNR2L3	chr20	57358447	57359498	-
PEA15	chr1	160205337	160215376	+
BOD1	chr5	173607145	173616659	-
TUBA1A	chr12	49184795	49189080	-
SPCS1	chr3	52704955	52711148	+
DGLUCY	chr14	91060333	91225632	+
GID8	chr20	62938147	62948475	+
ENSA	chr1	150600851	150629612	-
RSL24D1	chr15	55180806	55197049	-
ARPC2	chr2	218217141	218254356	+
ZNF431	chr19	21142024	21196053	+
MFGE8	chr15	88898683	88913381	-
MIF	chr22	23894383	23895227	+
MPC2	chr1	167916675	167937072	-
TNFRSF14	chr1	2555639	2565382	+
SOX8	chr16	981770	986979	+
PDZD8	chr10	117277274	117375440	-
BCR	chr22	23179704	23318037	+
AK2	chr1	33007940	33080996	-
AMACR	chr5	33986165	34008104	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-19b-3p	chr13	91351245	91351267	+
hsa-miR-27a-3p	chr19	13836447	13836467	-
hsa-miR-27b-3p	chr9	95085505	95085525	+
hsa-miR-301a-3p	chr17	59151149	59151171	-
hsa-miR-431-5p	chr14	100881026	100881046	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
SCARNA9	chr11	93721513	93721865	+
SNHG16	chr17	76557764	76565348	+

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.