exRNAdisease

General Information

Database ID:

exR0000370

RNA Name:

AGFG1

RNA Type:

mRNA

Chromosome:

chr2

Starnd:

Coordinate:

Start Site(bp):

227472152

End Site(bp):

227561214

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
MTRNR2L4	chr16	3370979	3372668	-
MRPS7	chr17	75261674	75266376	+
PCDH7	chr4	30720415	31146805	+
GNAS	chr20	58839718	58911192	+
COMMD1	chr2	61888724	62147247	+
FLOT2	chr17	28879335	28897733	-
UBE2W	chr8	73780097	73878910	-
C6orf47	chr6	31658298	31660778	-
TUBA1B	chr12	49127782	49131397	-
P2RX1	chr17	3896592	3916476	-
NDUFS7	chr19	1383527	1395589	+
BRD3	chr9	134030305	134068535	-
CCDC127	chr5	196868	218153	-
LAMP1	chr13	113297239	113323672	+
LSP1	chr11	1852970	1892267	+
RPSA	chr3	39406716	39412542	+
PIP4K2C	chr12	57591174	57603418	+
RACK1	chr5	181236897	181248096	-
EZH2	chr7	148807383	148884321	-
MEF2A	chr15	99565417	99716466	+
BSG	chr19	571277	583493	+
REXO1	chr19	1815248	1848483	-
ID1	chr20	31605283	31606515	+
MXD4	chr4	2247432	2262109	-
RPL27A	chr11	8682788	8714759	+
FEM1B	chr15	68277745	68295862	+
RPS23	chr5	82273320	82278396	-
AC116366.3	chr5	132410832	132646079	+
MRPL10	chr17	47823272	47831541	-
ATP5MPL	chr14	103912288	103928269	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-106b-5p	chr7	100094043	100094063	-
hsa-miR-380-3p	chr14	101025056	101025077	+
hsa-miR-1270	chr19	20399320	20399342	-
hsa-miR-4492	chr11	118910765	118910781	+
hsa-miR-5703	chr2	227472162	227472179	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AD000090.1	chr19	35557956	35581954	+
AP001330.4	chr8	101208148	101208558	+
GAS5	chr1	173858559	173868882	-
HOXA-AS2	chr7	27107777	27134302	+
NEAT1	chr11	65422774	65445540	+
XIST	chrX	73820649	73852723	-

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.