exRNAdisease

General Information

Database ID:

exR0000121

RNA Name:

ACAP1

RNA Type:

mRNA

Chromosome:

chr17

Starnd:

Coordinate:

Start Site(bp):

7336529

End Site(bp):

7351477

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
HLA-DRA	chr6	32439878	32445046	+
FOXH1	chr8	144473412	144475849	-
ZNF449	chrX	135344796	135363413	+
MIF	chr22	23894383	23895227	+
KDF1	chr1	26949562	26960468	-
SQSTM1	chr5	179806398	179838078	+
PFN1	chr17	4945652	4949061	-
CD74	chr5	150400041	150412929	-
RGS10	chr10	119499817	119542719	-
TUBB	chr6	30720352	30725426	+
ISG15	chr1	1001138	1014540	+
C20orf204	chr20	64034344	64039962	+
AL133352.1	chr10	100505628	100529881	-
DHX16	chr6	30653119	30673006	-
AP002990.1	chr11	62559603	62591531	-
UGCG	chr9	111896814	111935369	+
DNAJC30	chr7	73680918	73683453	-
ACTG1	chr17	81509971	81523847	-
VPS53	chr17	508668	721717	-
HLA-DMA	chr6	32948613	32969094	-
CDC25B	chr20	3786772	3806121	+
RCC1	chr1	28505943	28539300	+
YME1L1	chr10	27110112	27155266	-
REEP3	chr10	63521401	63625128	+
CD70	chr19	6583183	6604103	-
ZNF593	chr1	26169908	26170873	+
NSMF	chr9	137447573	137459334	-
EXOC3	chr5	443175	471937	+
ZNF761	chr19	53445001	53458261	+
APH1A	chr1	150265399	150269580	-

miRNA targets:

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC139149.1	chr17	81514047	81527776	+
LINC01184	chr5	127939152	128083172	-
SNHG3	chr1	28505980	28510892	+

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.