exRNAdisease

General Information

Database ID:

exR0015886

RNA Name:

USP22

RNA Type:

mRNA

Chromosome:

chr17

Starnd:

Coordinate:

Start Site(bp):

20999596

End Site(bp):

21043760

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
AARS2	chr6	44298731	44313347	-
ABCB1	chr7	87503017	87713323	-
AC005726.1	chr17	28455752	28614185	-
AC008581.2	chr5	77030902	77152155	+
AC008695.1	chr5	131425891	131796983	-
AC010422.3	chr19	12643831	12648397	-
AC138811.2	chr16	18788063	18801519	-
ACBD3	chr1	226144679	226186741	-
ACIN1	chr14	23058564	23095614	-
ACLY	chr17	41866917	41930542	-
ADH5	chr4	99070978	99088801	-
ADSL	chr22	40346500	40390463	+
AGGF1	chr5	77029251	77065234	+
AHCY	chr20	34280268	34311802	-
AKR1B1	chr7	134442356	134459284	-
AL022238.4	chr22	40346529	40410054	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-148b-3p	chr12	54337278	54337299	+
hsa-miR-485-5p	chr14	101055427	101055448	+
hsa-miR-650	chr22	22822791	22822811	+
hsa-miR-371a-5p	chr19	53787680	53787699	+
hsa-miR-616-3p	chr12	57519183	57519204	-
hsa-miR-665	chr14	100875075	100875094	+
hsa-miR-1321	chrX	85835832	85835849	+
hsa-miR-4508	chr15	23562107	23562123	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC006064.5	chr12	6510275	6510522	+
AC007952.4	chr17	19112000	19112636	-
AC011445.1	chr19	39314651	39320858	-
AC016876.2	chr17	7581964	7584086	-
AC026362.1	chr12	122975320	122982907	+
AC067852.1	chr17	42536510	42562062	+
AC067930.1	chr8	143579636	143580670	+
AC087190.3	chr16	9104848	9113181	+
AC111170.2	chr17	77469162	77472770	-
AC133644.3	chr2	87455476	87767359	+
AD000090.1	chr19	35557956	35581954	+
AL022311.1	chr22	37876148	37895563	+

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.