exRNAdisease

Entry Detail

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General Information

Database ID: exR0015682 RNA Name: UBE2D3 RNA Type: mRNA Chromosome: chr4 Starnd: - Coordinate: Start Site(bp): 102794383 End Site(bp): 102868896 External Links: ENSG00000109332

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 AATF chr17 36948954 37056871 + ABCB7 chrX 75051048 75156732 - AC010422.3 chr19 12643831 12648397 - AC017083.3 chr2 68131238 68261230 - AC022384.1 chr3 10249372 10285796 + AC084337.2 chr11 6481485 6508978 + AC092143.1 chr16 89919165 89936092 + ACACA chr17 37084992 37406836 - ACSL3 chr2 222860942 222944639 + ACTB chr7 5527148 5563784 - ACTR3 chr2 113890063 113962596 + ACTR6 chr12 100199122 100241865 + ACYP1 chr14 75053237 75069483 - ADD3 chr10 109996368 110135565 + ADGRV1 chr5 90529344 91164437 + AGL chr1 99850361 99924023 + AHCYL1 chr1 109984765 110023742 + AHSA1 chr14 77457870 77469472 + AIF1L chr9 131096476 131123152 + AK4 chr1 65147549 65232145 + AKIRIN2 chr6 87674860 87702233 - AKR1A1 chr1 45550543 45570049 + ALDOA chr16 30064164 30070457 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC009133.5 chr16 29808679 29812227 + AC020663.1 chr16 4730115 4752565 - AL117378.1 chr6 131901963 131920565 + 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.