exRNAdisease

General Information

Database ID:

exR0015579

RNA Name:

TUBB

RNA Type:

mRNA

Chromosome:

chr6

Starnd:

Coordinate:

Start Site(bp):

30720352

End Site(bp):

30725426

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
AIF1L	chr9	131096476	131123152	+
AHI1	chr6	135283532	135497765	-
AC091959.3	chr5	146203550	146339251	+
ADGRL2	chr1	81306160	81992436	+
AL022238.4	chr22	40346529	40410054	+
ACADS	chr12	120725774	120740008	+
AC015813.2	chr17	57989038	58007246	-
AATF	chr17	36948954	37056871	+
AACS	chr12	125065434	125143333	+
AKR1A1	chr1	45550543	45570049	+
AC025165.3	chr12	57772660	57797554	+
ADGRV1	chr5	90529344	91164437	+
AGO1	chr1	35869808	35930532	+
ABHD10	chr3	111979010	111993368	+
AC010132.3	chr7	42909273	42932174	-
ACAP1	chr17	7336529	7351477	+
AC048338.1	chr12	122207779	122266423	-
AC006030.1	chr2	74211604	74363377	-
ADH5	chr4	99070978	99088801	-
ACBD6	chr1	180269653	180502954	-
AAMP	chr2	218264123	218270257	-
AIG1	chr6	143060496	143341058	+
ACTB	chr7	5527148	5563784	-
AC013394.1	chr15	92883413	92949230	+
AL590132.1	chr1	210858125	211134146	-
AHSA1	chr14	77457870	77469472	+
ALDH18A1	chr10	95605941	95656711	-
AKAP8	chr19	15353385	15379798	-
ACTG1	chr17	81509971	81523847	-
ACTR3	chr2	113890063	113962596	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-92a-3p	chrX	134169544	134169565	-
hsa-miR-3198	chr12	54231407	54231428	-
hsa-miR-3654	chr7	133034860	133034878	-

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AC002470.2	chr22	20979462	20998121	+
AC004687.1	chr17	58330884	58332508	-
AC010729.1	chr2	5726253	5730355	+
AC012360.3	chr2	105334027	105337475	-
AC016876.2	chr17	7581964	7584086	-
AC019205.1	chr6	73263212	73301789	+
AC022167.2	chr16	8848105	8860456	+
AC023509.1	chr12	53441741	53467528	+
AC026362.1	chr12	122975320	122982907	+
AC068134.1	chr2	232379635	232381674	-
AC092171.3	chr7	5426277	5428927	-
AC099522.2	chr5	73497550	73498293	-
AC114271.1	chr19	10333436	10336248	+
AC245014.3	chr1	145281116	145281462	+
AD000090.1	chr19	35557956	35581954	+
AL022311.1	chr22	37876148	37895563	+
AL023653.1	chrX	129794994	129796963	+
AL049543.1	chr6	28587378	28591747	+
AL132780.1	chr14	22929607	22956374	+
AL133215.2	chr10	101060029	101061005	-
AL137058.2	chr13	52600042	52642542	+
AL137127.1	chr1	19072110	19075511	-

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.