exRNAdisease

General Information

Database ID:

exR0012338

RNA Name:

RPL27

RNA Type:

mRNA

Chromosome:

chr17

Starnd:

Coordinate:

Start Site(bp):

42998273

End Site(bp):

43002959

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
AAAS	chr12	53307456	53324864	-
AAGAB	chr15	67200667	67255195	-
AARSD1	chr17	42950526	42964498	-
AC010422.3	chr19	12643831	12648397	-
AC018523.2	chr11	14493783	14520344	-
AC025165.3	chr12	57772660	57797554	+
AC092073.1	chr19	34396315	34409364	+
AC093525.2	chr16	2496032	2520218	+
AC138811.2	chr16	18788063	18801519	-
AC245033.1	chr15	82536788	82573194	-
ACADM	chr1	75724347	75787575	+
ACO1	chr9	32384603	32454769	+
ACOT11	chr1	54542257	54639192	+
ACSS1	chr20	25006230	25058980	-
ACTB	chr7	5527148	5563784	-
ACTG1	chr17	81509971	81523847	-
ACTR2	chr2	65227753	65271253	+
ACVR2B	chr3	38453890	38493142	+
ADM5	chr19	49688664	49690575	+
AFTPH	chr2	64524305	64593005	+
AIF1L	chr9	131096476	131123152	+
AIMP1	chr4	106315544	106349456	+
AKAP10	chr17	19904302	19978343	-
AL121594.1	chr14	35122549	35317474	+
AL358113.1	chr9	69035747	69255187	+
AL365205.1	chr6	41780349	41790141	+
ALDOA	chr16	30064164	30070457	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-142-3p	chr17	58331245	58331267	-
hsa-miR-302d-3p	chr4	112648006	112648028	-
hsa-miR-4485-3p	chr11	10508277	10508296	-
hsa-miR-7705	chr8	100703002	100703024	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC004687.1	chr17	58330884	58332508	-
AC007952.4	chr17	19112000	19112636	-
AC016027.1	chr22	18076527	18078884	-
AC020663.1	chr16	4730115	4752565	-
AC026362.1	chr12	122975320	122982907	+
AC084082.1	chr8	66112667	66126632	+
AC108134.2	chr16	3156736	3157483	-
AC245033.4	chr15	82533175	82540008	-
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.