exRNAdisease

General Information

Database ID:

exR0000096

RNA Name:

ABL2

RNA Type:

mRNA

Chromosome:

chr1

Starnd:

Coordinate:

Start Site(bp):

179099330

End Site(bp):

179229684

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
FBXL19	chr16	30923055	30948783	+
AC010422.3	chr19	12643831	12648397	-
SRPK2	chr7	105110704	105399308	-
KIAA0753	chr17	6578147	6640711	-
WDR74	chr11	62832342	62841809	-
RPL11	chr1	23691742	23696835	+
DNAH1	chr3	52316319	52400491	+
APBB3	chr5	140558268	140564781	-
HECTD4	chr12	112160188	112382439	-
RPS3	chr11	75399515	75422280	+
ARPP19	chr15	52547045	52569883	-
INPPL1	chr11	72223701	72239147	+
LRWD1	chr7	102464956	102473168	+
KPNA5	chr6	116681187	116741867	+
RPL12	chr9	127447674	127451406	-
KMT2D	chr12	49018975	49059774	-
UGDH	chr4	39498755	39528311	-
ZC4H2	chrX	64915802	65034713	-
PTMA	chr2	231706895	231713541	+
PDPN	chr1	13583465	13617957	+
CHCHD10	chr22	23765834	23768443	-
FUCA2	chr6	143494812	143511720	-
TEAD3	chr6	35473597	35497079	-
HNRNPM	chr19	8444767	8489114	+
ABL1	chr9	130713016	130887675	+
GLUL	chr1	182381704	182392206	-
UBR4	chr1	19074510	19210266	-
SSR2	chr1	156009048	156020951	-
RPL13A	chr19	49487554	49492308	+
IMP4	chr2	130342877	130347967	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-154-5p	chr14	101059769	101059790	+
hsa-miR-188-5p	chrX	50003517	50003537	+
hsa-miR-339-5p	chr7	1022990	1023012	-
hsa-miR-625-5p	chr14	65471116	65471136	+
hsa-miR-425-5p	chr3	49020199	49020221	-
hsa-miR-532-3p	chrX	50003204	50003225	+
hsa-miR-1224-5p	chr3	184241405	184241423	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
HIPK1-AS1	chr1	113924000	113929495	-
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.