exRNAdisease

General Information

Database ID:

exR0000467

RNA Name:

AKT1S1

RNA Type:

mRNA

Chromosome:

chr19

Starnd:

Coordinate:

Start Site(bp):

49869033

End Site(bp):

49878459

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
YIPF3	chr6	43511832	43516985	-
FOXRED2	chr22	36487190	36507101	-
FAM86C1	chr11	71787510	71801237	+
BABAM2	chr2	27889941	28338901	+
PABPN1	chr14	23321289	23326185	+
BBS10	chr12	76344474	76348415	-
ESYT1	chr12	56118250	56144671	+
ZNF585A	chr19	37106734	37172741	-
SEC62	chr3	169966635	169998373	+
EEF1G	chr11	62559596	62574086	-
SEPHS1	chr10	13317428	13348298	-
STAG3	chr7	100177563	100221488	+
CBX1	chr17	48070052	48101478	-
KIAA2013	chr1	11919591	11926428	-
IRF2BP2	chr1	234604269	234609525	-
NOMO3	chr16	16232528	16294811	+
KAT7	chr17	49788681	49835026	+
ZFP36L1	chr14	68787660	68796253	-
PODXL	chr7	131500262	131558217	-
CRABP2	chr1	156699606	156705816	-
PILRB	chr7	100352176	100367733	+
AGO2	chr8	140520156	140635633	-
DPY19L1	chr7	34928876	35038271	-
ATF5	chr19	49928702	49933935	+
ID1	chr20	31605283	31606515	+
MYL6	chr12	56158161	56163496	+
TMEM256-PLSCR3	chr17	7389734	7404097	-
SLC6A6	chr3	14402576	14489349	+
NLRX1	chr11	119166568	119184016	+
HNRNPUL1	chr19	41262496	41307787	+

miRNA targets:

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC113189.2	chr17	7420103	7444081	+
AC113189.4	chr17	7439506	7445966	+
AC079949.1	chr12	127142029	127146532	-
AP001626.1	chr21	42648271	42651244	-
HCG18	chr6	30286690	30327382	-
SLX1A-SULT1A3	chr16	30193892	30204310	+
STAG3L5P-PVRIG2P-PILRB	chr7	100336104	100367831	+
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.