exRNAdisease

General Information

Database ID:

exR0000436

RNA Name:

AKAP10

RNA Type:

mRNA

Chromosome:

chr17

Starnd:

Coordinate:

Start Site(bp):

19904302

End Site(bp):

19978343

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
TCERG1	chr5	146447311	146511961	+
EFNB2	chr13	106489745	106535662	-
MCFD2	chr2	46901870	46941855	-
ZNF850	chr19	36714383	36772825	-
ATP5MC2	chr12	53632726	53677408	-
PTPRF	chr1	43525187	43623666	+
NSMF	chr9	137447573	137459334	-
GUF1	chr4	44678420	44700928	+
AMPD2	chr1	109616104	109632053	+
MTG2	chr20	62183029	62203568	+
AASDHPPT	chr11	106075501	106098699	+
PROM1	chr4	15963076	16084378	-
RPL27	chr17	42998273	43002959	+
MICALL1	chr22	37905657	37942822	+
ZNF24	chr18	35332227	35345482	-
CSNK1E	chr22	38290691	38318084	-
ICMT	chr1	6221193	6235972	-
ZFAND3	chr6	37819727	38154624	+
SBNO2	chr19	1107637	1174268	-
OGT	chrX	71533104	71575892	+
FOXK2	chr17	82519713	82644662	+
CANX	chr5	179678628	179731641	+
VMP1	chr17	59707192	59842255	+
CREBL2	chr12	12611827	12645108	+
GIGYF2	chr2	232697299	232860575	+
TNFSF9	chr19	6531026	6535924	+
SOBP	chr6	107490106	107661306	+
AP2A2	chr11	924894	1012245	+
SLC35F2	chr11	107790991	107928293	-
AP002990.1	chr11	62559603	62591531	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-130a-3p	chr11	57641252	57641273	+
hsa-miR-130b-3p	chr22	21653354	21653375	+
hsa-miR-454-3p	chr17	59137787	59137809	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC079949.1	chr12	127142029	127146532	-
AL645608.1	chr1	1011997	1013193	-
TMEM147-AS1	chr19	35540738	35546029	-

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.