exRNAdisease

General Information

Database ID:

exR0000103

RNA Name:

ABRACL

RNA Type:

mRNA

Chromosome:

chr6

Starnd:

Coordinate:

Start Site(bp):

139028745

End Site(bp):

139043302

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
FGFBP3	chr10	91906584	91909486	-
RPL11	chr1	23691742	23696835	+
STIL	chr1	47250139	47314147	-
BIRC6	chr2	32357028	32618899	+
EIF4A1	chr17	7572706	7579006	+
REPIN1	chr7	150368189	150374044	+
UBE2I	chr16	1308880	1327018	+
UTP18	chr17	51260546	51297936	+
EZR	chr6	158765741	158819368	-
RPS5	chr19	58386400	58394806	+
NUCKS1	chr1	205712822	205750182	-
APLP2	chr11	130068147	130144811	+
POMT1	chr9	131502902	131523806	+
DCLRE1B	chr1	113905213	113914086	+
MIF	chr22	23894383	23895227	+
CALR	chr19	12938578	12944489	+
XPO7	chr8	21919662	22006585	+
GOT1	chr10	99396870	99430624	-
TUBB	chr6	30720352	30725426	+
MEX3A	chr1	156072013	156082465	-
PXMP2	chr12	132687587	132704985	+
BABAM1	chr19	17267376	17281249	+
HSPB8	chr12	119178642	119221131	+
PER1	chr17	8140472	8156506	-
DHX32	chr10	125836337	125896436	-
APP	chr21	25880550	26171128	-
SLC38A2	chr12	46358188	46372773	-
NEDD9	chr6	11183298	11382348	-
S100A16	chr1	153606886	153613145	-
SENP3-EIF4A1	chr17	7563287	7578715	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-205-5p	chr1	209432166	209432187	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC016876.2	chr17	7581964	7584086	-
AL035458.2	chr20	34234840	34281173	-
AC135586.2	chr12	132688049	132714912	+
AL359924.1	chr1	237862175	237928321	+
AP006621.3	chr11	777578	784297	+
MAPKAPK5-AS1	chr12	111839764	111842902	-
NEAT1	chr11	65422774	65445540	+

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.