exRNAdisease

General Information

Database ID:

exR0003718

RNA Name:

DDB1

RNA Type:

mRNA

Chromosome:

chr11

Starnd:

Coordinate:

Start Site(bp):

61299451

End Site(bp):

61342596

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
AAMP	chr2	218264123	218270257	-
ABCB8	chr7	151028422	151047782	+
ABI2	chr2	203328239	203447728	+
ABRACL	chr6	139028745	139043302	+
AC005258.1	chr19	2269525	2341172	+
AC008982.1	chr19	38817471	38840178	-
AC011448.1	chr19	19516227	19536076	+
AC118549.1	chr1	77562416	77683419	-
ACBD6	chr1	180269653	180502954	-
ACIN1	chr14	23058564	23095614	-
ACSL1	chr4	184755595	184826818	-
ACTB	chr7	5527148	5563784	-
ACTG1	chr17	81509971	81523847	-
ACTR3	chr2	113890063	113962596	+
ACTR8	chr3	53867066	53882152	-
ADAMTS1	chr21	26835755	26845409	-
ADAR	chr1	154582057	154628013	-
ADGRG6	chr6	142301854	142446266	+
AGO2	chr8	140520156	140635633	-
AGPAT4	chr6	161129967	161274061	-
AJUBA	chr14	22971177	22982551	-
AKR7A2	chr1	19303965	19312146	-
AKT1	chr14	104769349	104795751	-
AKT1S1	chr19	49869033	49878459	-
AL133352.1	chr10	100505628	100529881	-
AL136454.1	chr1	192716132	192716653	+
AL139011.2	chr1	160216800	160285130	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-155-5p	chr21	25573983	25574006	+
hsa-miR-367-3p	chr4	112647877	112647898	-
hsa-miR-155-3p	chr21	25574022	25574043	+
hsa-miR-4426	chr1	192716333	192716349	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC012485.1	chr2	238231684	238255633	+
AC016876.2	chr17	7581964	7584086	-
AC020663.1	chr16	4730115	4752565	-
AC124068.2	chr15	89335053	89336161	+
AC133644.3	chr2	87455476	87767359	+
AD000090.1	chr19	35557956	35581954	+
AL022311.1	chr22	37876148	37895563	+

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.