exRNAdisease

General Information

Database ID:

exR0007738

RNA Name:

LCP1

RNA Type:

mRNA

Chromosome:

chr13

Starnd:

Coordinate:

Start Site(bp):

46125920

End Site(bp):

46211871

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	-
AC004922.1	chr7	99325879	99394653	+
AC008982.1	chr19	38817471	38840178	-
AC012254.2	chr18	47108188	47176345	-
AC023055.1	chr12	55757275	55827546	-
ACAP2	chr3	195274745	195443044	-
ACBD5	chr10	27195214	27242130	-
ACP1	chr2	264140	278283	+
ACSS1	chr20	25006230	25058980	-
ACTB	chr7	5527148	5563784	-
ACTBL2	chr5	57480018	57482811	-
ACTG1	chr17	81509971	81523847	-
ACTR3C	chr7	150243916	150323725	-
ADAR	chr1	154582057	154628013	-
ADSL	chr22	40346500	40390463	+
AFG3L2	chr18	12328944	12377227	-
AFTPH	chr2	64524305	64593005	+
AGPAT4	chr6	161129967	161274061	-
AHSA1	chr14	77457870	77469472	+
AKR1A1	chr1	45550543	45570049	+
AL021546.1	chr12	120438198	120460006	+
AL022238.4	chr22	40346529	40410054	+
AL109827.1	chr20	35632340	35674544	-
AL139300.1	chr14	103562962	103685924	+
ALAS1	chr3	52198086	52214327	+
ALDOA	chr16	30064164	30070457	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-155-5p	chr21	25573983	25574006	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC006064.5	chr12	6510275	6510522	+
AC026202.2	chr3	5156905	5187329	-
AC026202.3	chr3	5187172	5188298	-
AC055860.1	chr11	18000542	18022931	-
AC079781.5	chr7	97851688	97972985	-
AC135048.1	chr16	30948386	30956511	+
AC245014.3	chr1	145281116	145281462	+
AL022311.1	chr22	37876148	37895563	+
AL137058.2	chr13	52600042	52642542	+

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.