exRNAdisease

General Information

Database ID:

exR0002073

RNA Name:

CBS

RNA Type:

mRNA

Chromosome:

chr21

Starnd:

Coordinate:

Start Site(bp):

43053191

End Site(bp):

43076943

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
ABHD16A	chr6	31686955	31703356	-
ABHD4	chr14	22598237	22613215	+
ABHD5	chr3	43690108	43734371	+
AC010323.1	chr19	8308283	8321379	-
AC010422.5	chr19	12664828	12669397	-
AC135050.2	chr16	31083439	31094956	-
AC138811.2	chr16	18788063	18801519	-
AC139530.2	chr17	81703371	81720539	+
AC245033.1	chr15	82536788	82573194	-
ACKR3	chr2	236567787	236582354	+
ACTA1	chr1	229431245	229434098	-
ACTG1	chr17	81509971	81523847	-
ACTR1A	chr10	102461881	102502712	-
ACTR3	chr2	113890063	113962596	+
ADRM1	chr20	62302093	62308862	+
AGBL5	chr2	27042364	27070622	+
AKAP1	chr17	57085092	57121346	+
AKR1A1	chr1	45550543	45570049	+
AL132780.3	chr14	22946270	22982258	-
AL162417.1	chr9	133098121	133163914	-
ALDH9A1	chr1	165662216	165698863	-
ALDOA	chr16	30064164	30070457	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-6853-3p	chr9	35732974	35732995	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC004951.4	chr7	43951910	44019151	-
AC026461.1	chr16	56682470	56687807	+
AC069281.2	chr7	100572232	100578700	-
AC074044.1	chr3	112990447	112991153	-
AC245033.4	chr15	82533175	82540008	-
AD000090.1	chr19	35557956	35581954	+
AL049796.1	chr1	93847174	93848939	+

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.