exRNAdisease

General Information

Database ID:

exR0000353

RNA Name:

AFMID

RNA Type:

mRNA

Chromosome:

chr17

Starnd:

Coordinate:

Start Site(bp):

78187317

End Site(bp):

78207701

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
ALDOA	chr16	30064164	30070457	+
C8orf88	chr8	90958471	90985238	-
CCT7	chr2	73233420	73253021	+
CFL1	chr11	65823022	65862026	-
CNOT1	chr16	58519951	58629885	-
CRYBG2	chr1	26321698	26360080	-
CSRP2	chr12	76858709	76879023	-
EEF1D	chr8	143579697	143599541	-
FLNA	chrX	154348524	154374638	-
GTPBP3	chr19	17334920	17342731	+
HLA-DPB1	chr6	33075990	33089696	+
HOXD9	chr2	176122719	176124937	+
LMNB1	chr5	126776623	126837020	+
LPCAT1	chr5	1456480	1523962	-
MAP3K11	chr11	65597756	65615382	-
MYO1C	chr17	1464186	1492686	-
NCBP3	chr17	3802158	3846246	-
PCNP	chr3	101574180	101594465	+
PPIA	chr7	44796680	44824564	+
RANBP2	chr2	108719482	108785809	+
RBM5	chr3	50088919	50119021	+
SIPA1L1	chr14	71320449	71741229	+
SRA1	chr5	140537340	140558252	-
TLR7	chrX	12867072	12890361	+
UHRF1BP1	chr6	34792015	34883138	+
UQCRHL	chr1	15807169	15809348	-
USF2	chr19	35268962	35279821	+

miRNA targets:

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AL021707.3	chr22	38734730	38738990	+
RMRP	chr9	35657751	35658018	-

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.