exRNAdisease

General Information

Database ID:

exR0000275

RNA Name:

ADARB1

RNA Type:

mRNA

Chromosome:

chr21

Starnd:

Coordinate:

Start Site(bp):

45073853

End Site(bp):

45226560

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
UBB	chr17	16380798	16382745	+
LBHD1	chr11	62662817	62672255	-
TNPO2	chr19	12699194	12724011	-
TXNRD2	chr22	19875517	19941820	-
TMEM131	chr2	97756333	97995948	-
EXOSC10	chr1	11066618	11099869	-
IFT140	chr16	1510427	1612072	-
ZFR	chr5	32354350	32444740	-
RPL37A	chr2	216498825	216579180	+
RAC2	chr22	37225270	37244448	-
IGF1R	chr15	98648539	98964530	+
CAD	chr2	27217369	27243943	+
WDR45B	chr17	82614562	82648553	-
HMGA1	chr6	34236873	34246231	+
SLC9A3R1	chr17	74748628	74769353	+
PSMA4	chr15	78540405	78552417	+
MYCN	chr2	15940550	15947007	+
MAPK12	chr22	50245450	50261716	-
RPS14	chr5	150442635	150449739	-
PIP4K2C	chr12	57591174	57603418	+
PIP5K1A	chr1	151197949	151249536	+
SYNJ2BP-COX16	chr14	70326064	70417074	-
AC120114.4	chr16	29817239	29830627	+
RANBP1	chr22	20115938	20127355	+
COASY	chr17	42561467	42566277	+
HNRNPU	chr1	244840638	244864560	-
GFOD2	chr16	67674531	67719339	-
SPON1	chr11	13962723	14268133	+
COX16	chr14	70325081	70416984	-
AUTS2	chr7	69598296	70793506	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-17-5p	chr13	91350618	91350640	+
hsa-miR-20a-5p	chr13	91351072	91351094	+
hsa-miR-93-5p	chr7	100093815	100093837	-
hsa-miR-106a-5p	chrX	134170244	134170266	-
hsa-miR-301a-3p	chr17	59151149	59151171	-
hsa-miR-20b-5p	chrX	134169850	134169872	-
hsa-miR-512-3p	chr19	53666729	53666750	+
hsa-miR-454-3p	chr17	59137787	59137809	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
SNHG7	chr9	136721366	136728184	-

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.