exRNAdisease

General Information

Database ID:

exR0000450

RNA Name:

AKIP1

RNA Type:

mRNA

Chromosome:

chr11

Starnd:

Coordinate:

Start Site(bp):

8911139

End Site(bp):

8920084

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
CBX3	chr7	26201162	26213607	+
FSCN1	chr7	5592816	5606655	+
MDM2	chr12	68808177	68850686	+
OAS3	chr12	112938444	112973251	+
COPS7B	chr2	231781671	231809254	+
EIF1	chr17	41688885	41692668	+
MRPL49	chr11	65122183	65127371	+
SLC2A1	chr1	42925375	42958868	-
B2M	chr15	44711487	44718877	+
NIPSNAP1	chr22	29554808	29581327	-
AK4	chr1	65147549	65232145	+
SLC25A6	chrX	1386152	1392113	-
DHX15	chr4	24517441	24584554	-
VLDLR	chr9	2621787	2660056	+
AL136454.1	chr1	192716132	192716653	+
TXNL1	chr18	56597209	56651600	-
CHKB-CPT1B	chr22	50568869	50582965	-
KRT7	chr12	52232520	52252186	+
TAGLN2	chr1	159918107	159925732	-
CHMP1A	chr16	89644435	89657721	-
FP565260.6	chr21	5155499	5165472	-
FP565260.2	chr21	5116343	5133805	-
OST4	chr2	27070472	27071654	-
TSTD2	chr9	97600080	97633368	-
PSMA5	chr1	109399042	109426448	-
PPP2R1A	chr19	52190048	52229518	+
IL21R	chr16	27402174	27452042	+
THOC5	chr22	29505879	29555216	-
GPSM3	chr6	32190766	32195523	-
MAT2A	chr2	85539168	85545281	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-4426	chr1	192716333	192716349	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
DANCR	chr4	52712404	52720351	+

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.