exRNAdisease

General Information

Database ID:

exR0007706

RNA Name:

LASP1

RNA Type:

mRNA

Chromosome:

chr17

Starnd:

Coordinate:

Start Site(bp):

38869859

End Site(bp):

38921770

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
ABHD14A-ACY1	chr3	51974706	51989183	+
AC007192.1	chr19	18153158	18178117	+
AC010422.3	chr19	12643831	12648397	-
AC010463.1	chr19	17267418	17282966	+
AC073896.1	chr12	56285916	56316059	-
AC093323.1	chr4	6663396	6676755	+
ACTG1	chr17	81509971	81523847	-
ACTR1B	chr2	97655939	97664044	-
ACY1	chr3	51983340	51989197	+
ADAR	chr1	154582057	154628013	-
ADM	chr11	10305073	10307397	+
AGFG2	chr7	100539203	100568220	+
AHCYL1	chr1	109984765	110023742	+
AIF1L	chr9	131096476	131123152	+
AKAP17A	chrX	1591604	1602520	+
AL022238.4	chr22	40346529	40410054	+
AL121845.3	chr20	63708864	63739103	+
AL132780.3	chr14	22946270	22982258	-
AL139011.2	chr1	160216800	160285130	-
ALDH18A1	chr10	95605941	95656711	-
ALDH5A1	chr6	24494867	24537207	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-28-5p	chr3	188688794	188688815	+
hsa-miR-147a	chr9	120244985	120245004	-
hsa-miR-27b-3p	chr9	95085505	95085525	+
hsa-miR-206	chr6	52144401	52144422	+
hsa-miR-342-3p	chr14	100109715	100109737	+
hsa-miR-193b-3p	chr16	14304017	14304038	+
hsa-miR-296-3p	chr20	58817626	58817647	-
hsa-miR-423-5p	chr17	30117095	30117117	+
hsa-miR-873-5p	chr9	28888925	28888945	-
hsa-miR-1224-5p	chr3	184241405	184241423	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC091564.7	chr11	6610883	6616594	-
AC132217.1	chr11	2129121	2129964	-

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.