exRNAdisease

General Information

Database ID:

exR0000380

RNA Name:

AGPAT1

RNA Type:

mRNA

Chromosome:

chr6

Starnd:

Coordinate:

Start Site(bp):

32168212

End Site(bp):

32178096

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
NAP1L3	chrX	93670930	93673578	-
UBC	chr12	124911604	124917368	-
ENO1	chr1	8861000	8879190	-
TRIM71	chr3	32817997	32897824	+
NEMP1	chr12	57055643	57088063	-
DBN1	chr5	177456608	177474401	-
DAG1	chr3	49468703	49535618	+
ABHD17C	chr15	80679684	80755621	+
ATR	chr3	142449007	142578733	-
MT-ND1	chrMT	3307	4262	+
SNRNP200	chr2	96274338	96321271	-
TMPO	chr12	98515512	98550379	+
DHFR	chr5	80626226	80654983	-
PAK6	chr15	40217428	40277487	+
NEK6	chr9	124257606	124353307	+
APP	chr21	25880550	26171128	-
GMPS	chr3	155870650	155944020	+
ACTG1	chr17	81509971	81523847	-
MFSD12	chr19	3538261	3574290	-
RPS3	chr11	75399515	75422280	+
RAI1	chr17	17681458	17811453	+
CBX1	chr17	48070052	48101478	-
SDHC	chr1	161314257	161375340	+
AL121753.1	chr20	35267885	35280043	-
EDC4	chr16	67873052	67884499	+
PTPN12	chr7	77537295	77640069	+
COX7A2L	chr2	42333546	42425088	-
RPL31	chr2	101002229	101024032	+
ELF1	chr13	40931924	41061440	-
SIX4	chr14	60709539	60724351	-

miRNA targets:

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC040162.3	chr16	67882461	67886367	+
GATA3-AS1	chr10	8050450	8053484	-
OIP5-AS1	chr15	41283990	41309737	+
SNHG16	chr17	76557764	76565348	+
XIST	chrX	73820649	73852723	-
ZNF436-AS1	chr1	23368997	23371839	+

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.