exRNAdisease

General Information

Database ID:

exR0000350

RNA Name:

AFF4

RNA Type:

mRNA

Chromosome:

chr5

Starnd:

Coordinate:

Start Site(bp):

132875395

End Site(bp):

132963634

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
CCDC6	chr10	59788747	59906556	-
GAN	chr16	81314966	81380198	+
KCTD3	chr1	215567304	215621807	+
MAPK14	chr6	36027677	36111236	+
CDYL	chr6	4706159	4955551	+
KRAS	chr12	25205246	25250936	-
ANKHD1-EIF4EBP3	chr5	140401908	140549569	+
ARFGEF3	chr6	138161939	138344663	+
EIF3C	chr16	28688558	28735730	+
ENSA	chr1	150600851	150629612	-
UBA52	chr19	18571730	18577550	+
FCHSD1	chr5	141639302	141651418	-
BRK1	chr3	10115675	10127190	+
AC048338.1	chr12	122207779	122266423	-
GUCY1B1	chr4	155758992	155807774	+
RPLP1	chr15	69452814	69456205	+
SNRPA	chr19	40750637	40765389	+
MTX3	chr5	79976731	79991265	-
KCNN1	chr19	17951293	18000080	+
RHOG	chr11	3826978	3840959	-
TUBA1B	chr12	49127782	49131397	-
CSK	chr15	74782057	74803198	+
RHEB	chr7	151466012	151520120	-
NUCKS1	chr1	205712822	205750182	-
DEPDC1	chr1	68474152	68497221	-
EIF4EBP3	chr5	140547662	140549576	+
SMARCC1	chr3	47585269	47782106	-
HDHD2	chr18	47107408	47150500	-
NET1	chr10	5412557	5459056	+
HNRNPDL	chr4	82422564	82430408	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-20a-5p	chr13	91351072	91351094	+
hsa-miR-33a-5p	chr22	41900949	41900969	+
hsa-miR-93-5p	chr7	100093815	100093837	-
hsa-miR-205-5p	chr1	209432166	209432187	+
hsa-miR-106b-5p	chr7	100094043	100094063	-
hsa-miR-299-3p	chr14	101023832	101023853	+
hsa-miR-519c-5p	chr19	53686484	53686505	+
hsa-miR-526a-5p	chr19	53726928	53726949	+
hsa-miR-33b-5p	chr17	17813897	17813916	-
hsa-miR-642a-5p	chr19	45674943	45674964	+
hsa-miR-423-5p	chr17	30117095	30117117	+
hsa-miR-519b-5p	chr19	53695225	53695246	+
hsa-miR-520c-5p	chr19	53707468	53707489	+
hsa-miR-518d-5p	chr19	53734892	53734913	+
hsa-miR-1321	chrX	85835832	85835849	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC008105.3	chr17	45190931	45222222	-
AC091564.7	chr11	6610883	6616594	-
XIST	chrX	73820649	73852723	-

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.