exRNAdisease

General Information

Database ID:

exR0000279

RNA Name:

ADAT3

RNA Type:

mRNA

Chromosome:

chr19

Starnd:

Coordinate:

Start Site(bp):

1905399

End Site(bp):

1913447

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
STRN3	chr14	30893799	31026401	-
DBN1	chr5	177456608	177474401	-
NUDT19	chr19	32691961	32713796	+
STARD9	chr15	42575606	42720998	+
KRT18	chr12	52948871	52952906	+
JUND	chr19	18279694	18281622	-
MLLT6	chr17	38705273	38729795	+
TMEM256-PLSCR3	chr17	7389734	7404097	-
LARP1	chr5	154712843	154817605	+
SYMPK	chr19	45815410	45863194	-
SLC9A3R1	chr17	74748628	74769353	+
EXOSC2	chr9	130693721	130704894	+
TMEM132A	chr11	60924463	60937159	+
HNRNPAB	chr5	178204533	178211163	+
DHX38	chr16	72093613	72112912	+
HNRNPK	chr9	83968083	83980616	-
PLSCR3	chr17	7389727	7394842	-
RPS28	chr19	8321158	8323340	+
C5AR1	chr19	47290023	47322066	+
DZIP1	chr13	95578202	95644703	-
CIC	chr19	42268537	42295797	+
ZNF721	chr4	425815	499156	-
SRSF4	chr1	29147743	29181900	-
SIRPA	chr20	1894167	1940592	+
SCAMP4	chr19	1905372	1926013	+
ARAP1	chr11	72685069	72793599	-
RAN	chr12	130872037	130877678	+
HTT	chr4	3041422	3243960	+
PKMYT1	chr16	2968024	2980479	-
CYB5R3	chr22	42617840	42649392	-

miRNA targets:

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
MIRLET7BHG	chr22	46053869	46113928	+

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.