exRNAdisease

General Information

Database ID:

exR0000317

RNA Name:

ADNP

RNA Type:

mRNA

Chromosome:

chr20

Starnd:

Coordinate:

Start Site(bp):

50888916

End Site(bp):

50931437

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
HNRNPA3	chr2	177212563	177223958	+
GRPEL1	chr4	7058895	7068064	-
SNRPA	chr19	40750637	40765389	+
IL9R	chrX	155997581	156010817	+
RPLP0	chr12	120196699	120201235	-
COG8	chr16	69320140	69339667	-
CREBRF	chr5	173056352	173139284	+
RREB1	chr6	7107597	7251980	+
LMO2	chr11	33858576	33892076	-
HDGF	chr1	156742109	156766925	-
TUBA1B	chr12	49127782	49131397	-
ZFAND3	chr6	37819727	38154624	+
CUL9	chr6	43182184	43224587	+
SLC39A10	chr2	195575977	195737702	+
GATD1	chr11	767220	777488	-
POLR2B	chr4	56977722	57031158	+
HPS5	chr11	18278668	18322198	-
KDM3B	chr5	138352685	138437028	+
CCT3	chr1	156308968	156367873	-
ACOT9	chrX	23701055	23766475	-
MTCH1	chr6	36968141	36986298	-
LRP11	chr6	149818757	149864359	-
LMAN1	chr18	59327823	59359265	-
EIF4E2	chr2	232550674	232583644	+
CBL	chr11	119206298	119313926	+
ATP5MC3	chr2	175176258	175184607	-
C18orf25	chr18	46173553	46266992	+
MAP7D1	chr1	36155579	36180849	+
HMGA1	chr6	34236873	34246231	+
PRMT3	chr11	20387558	20509338	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-17-5p	chr13	91350618	91350640	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC023509.1	chr12	53441741	53467528	+
AJ271736.1	chrX	156004218	156022236	+
AC079949.1	chr12	127142029	127146532	-
MALAT1	chr11	65497688	65506516	+
MIR17HG	chr13	91347820	91354579	+
TUG1	chr22	30969245	30979395	+

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.