exRNAdisease

General Information

Database ID:

exR0000022

RNA Name:

AASS

RNA Type:

mRNA

Chromosome:

chr7

Starnd:

Coordinate:

Start Site(bp):

122073549

End Site(bp):

122144255

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
IRF3	chr19	49659569	49665875	-
CDK2	chr12	55966781	55972789	+
FUBP1	chr1	77944055	77979110	-
CDC34	chr19	531760	542092	+
AC010422.3	chr19	12643831	12648397	-
NDUFA4	chr7	10931943	10940153	-
ACTG1	chr17	81509971	81523847	-
C16orf70	chr16	67109941	67148544	+
AC015813.2	chr17	57989038	58007246	-
MATR3	chr5	139273752	139331671	+
QSOX1	chr1	180154869	180204030	+
FAR1	chr11	13668668	13732346	+
LMNB2	chr19	2427638	2456959	-
PKM	chr15	72199029	72231822	-
RPL18A	chr19	17859910	17864153	+
HDLBP	chr2	241227264	241317061	-
WDR3	chr1	117929720	117966543	+
ATP8B2	chr1	154325553	154351304	+
SLC25A5	chrX	119468422	119471396	+
SRSF5	chr14	69726900	69772005	+
ACTN1	chr14	68874143	68979440	-
ATP6V1G2-DDX39B	chr6	31530219	31546608	-
ADAMTS8	chr11	130404923	130428609	-
NASP	chr1	45583846	45618904	+
STX6	chr1	180972712	181023121	-
SLC25A28	chr10	99610522	99620609	-
RICTOR	chr5	38937920	39074399	-
LARP1	chr5	154712843	154817605	+
EIF3L	chr22	37848868	37889407	+
CMTM6	chr3	32481312	32502852	-

miRNA targets:

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC106864.1	chr4	112693047	112706810	-
AC138904.1	chr16	28284885	28292064	-
AL022311.1	chr22	37876148	37895563	+
AC068831.7	chr15	91022766	91023200	+
GABPB1-AS1	chr15	50354959	50372202	+
NORAD	chr20	36045618	36051018	-
ZBED3-AS1	chr5	77086688	77166909	+

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.