exRNAdisease

General Information

Database ID:

exR0007843

RNA Name:

LIN28A

RNA Type:

mRNA

Chromosome:

chr1

Starnd:

Coordinate:

Start Site(bp):

26410817

End Site(bp):

26429728

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
AHCYL2	chr7	129225023	129430211	+
AGAP1	chr2	235494043	236131800	+
ACKR3	chr2	236567787	236582354	+
AC131160.1	chr3	183815568	183884889	-
ACTR3B	chr7	152759749	152855378	+
AC006064.6	chr12	6556886	6607367	-
AC027644.4	chr7	66628958	66811189	+
AC008575.1	chr5	112827213	112867582	+
AASS	chr7	122073549	122144255	-
AC073508.2	chr17	40627356	40665141	-
ACOT2	chr14	73567620	73575658	+
ADAR	chr1	154582057	154628013	-
AC004832.3	chr22	30409255	30428990	+
ABCE1	chr4	145098288	145129524	+
AKAP8L	chr19	15380050	15419141	-
AKR7A2	chr1	19303965	19312146	-
ADCY2	chr5	7396138	7830081	+
AL139300.1	chr14	103562962	103685924	+
ALDH4A1	chr1	18871430	18902724	-
AK7	chr14	96392128	96489427	+
ABI2	chr2	203328239	203447728	+
AC007192.1	chr19	18153158	18178117	+
AL138752.2	chr9	37588413	38068687	-
AC118549.1	chr1	77562416	77683419	-
ACAA1	chr3	38103129	38137242	-
ADGRL1	chr19	14147743	14206187	-
ADD3	chr10	109996368	110135565	+
AK2	chr1	33007940	33080996	-
ABHD13	chr13	108218392	108234243	+
ACTB	chr7	5527148	5563784	-

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-3654	chr7	133034860	133034878	-
hsa-miR-664b-5p	chrX	154768596	154768619	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC009446.1	chr8	71675300	71702786	+
AC012615.1	chr19	1874871	1876169	-
AC016747.4	chr2	61115787	61164825	+
AC016876.2	chr17	7581964	7584086	-
AC106864.1	chr4	112693047	112706810	-
AC114284.1	chr5	120781218	120790778	+
AD000090.1	chr19	35557956	35581954	+
AL022311.1	chr22	37876148	37895563	+
AL137782.1	chr13	75549773	75807120	+

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.