exRNAdisease

General Information

Database ID:

exR0000344

RNA Name:

AFAP1

RNA Type:

mRNA

Chromosome:

chr4

Starnd:

Coordinate:

Start Site(bp):

7758714

End Site(bp):

7939926

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
RAPGEF1	chr9	131576770	131740074	-
PGAM1	chr10	97426191	97433444	+
RBX1	chr22	40951347	40973309	+
ZNF462	chr9	106863166	107013634	+
DKC1	chrX	154762742	154777689	+
PA2G4	chr12	56104537	56113910	+
NCL	chr2	231453531	231483641	-
LAMTOR2	chr1	156054782	156058506	+
GAPDH	chr12	6534512	6538374	+
EXOSC4	chr8	144078648	144080648	+
RPS14	chr5	150442635	150449739	-
WDR46	chr6	33279108	33289247	-
TCP1	chr6	159778498	159789703	-
PITX2	chr4	110617423	110642123	-
FNDC3A	chr13	48975912	49209779	+
PFN1	chr17	4945652	4949061	-
FKBP1A	chr20	1368978	1393172	-
HS6ST1	chr2	128236716	128318868	-
DTL	chr1	212035553	212107400	+
TNIK	chr3	171058414	171460408	-
GDAP1	chr8	74321130	74488872	+
ACOX3	chr4	8366282	8440723	-
YME1L1	chr10	27110112	27155266	-
ERP29	chr12	112013348	112023449	+
MT-CO1	chrMT	5904	7445	+
PABPC4	chr1	39560816	39576790	-
MT-ND2	chrMT	4470	5511	+
BOD1	chr5	173607145	173616659	-
NUCKS1	chr1	205712822	205750182	-
SPG7	chr16	89490719	89557768	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-193a-3p	chr17	31560050	31560071	+
hsa-miR-485-5p	chr14	101055427	101055448	+
hsa-miR-193b-3p	chr16	14304017	14304038	+
hsa-miR-650	chr22	22822791	22822811	+
hsa-miR-423-5p	chr17	30117095	30117117	+
hsa-miR-664b-5p	chrX	154768596	154768619	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC016876.2	chr17	7581964	7584086	-
AL355987.4	chr9	136799223	136810042	+
SNHG14	chr15	24978583	25420336	+

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.