exRNAdisease

General Information

Database ID:

exR0008322

RNA Name:

MARCKSL1

RNA Type:

mRNA

Chromosome:

chr1

Starnd:

Coordinate:

Start Site(bp):

32333839

End Site(bp):

32336233

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
ABCD4	chr14	74285269	74303055	-
ABCF3	chr3	184186023	184194012	+
AC005832.4	chr12	4604944	4662643	+
AC008581.2	chr5	77030902	77152155	+
AC008982.1	chr19	38817471	38840178	-
AC010422.3	chr19	12643831	12648397	-
AC011448.1	chr19	19516227	19536076	+
AC012254.2	chr18	47108188	47176345	-
AC091959.3	chr5	146203550	146339251	+
ACAA1	chr3	38103129	38137242	-
ACACA	chr17	37084992	37406836	-
ACD	chr16	67657512	67660815	-
ACIN1	chr14	23058564	23095614	-
ACO2	chr22	41469117	41528989	+
ACTB	chr7	5527148	5563784	-
ACTG1	chr17	81509971	81523847	-
ACTR3	chr2	113890063	113962596	+
ADAM17	chr2	9488486	9556732	-
ADAMTS13	chr9	133414358	133459402	+
ADAMTS2	chr5	179110853	179345461	-
ADD1	chr4	2843857	2930076	+
ADIPOR1	chr1	202940826	202958572	-
AGGF1	chr5	77029251	77065234	+
AGL	chr1	99850361	99924023	+
AHDC1	chr1	27534035	27604431	-
AIF1L	chr9	131096476	131123152	+
AKT1	chr14	104769349	104795751	-
AL136454.1	chr1	192716132	192716653	+
AL365205.1	chr6	41780349	41790141	+
AL807752.6	chr9	137031241	137040436	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-let-7a-5p	chr9	94175962	94175983	+
hsa-let-7b-5p	chr22	46113691	46113712	+
hsa-let-7g-5p	chr3	52268336	52268357	-
hsa-miR-541-3p	chr14	101064548	101064569	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC026362.1	chr12	122975320	122982907	+
AC060780.1	chr17	43148368	43171037	-
AC067852.2	chr17	42552436	42554748	-
AC069281.2	chr7	100572232	100578700	-
AC097359.2	chr3	37241789	37244177	-
AC104257.1	chr8	131308545	131317632	+
AC112229.4	chr2	110386411	110433673	-

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.