exRNAdisease

Entry Detail

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General Information

Database ID: exR0000230 RNA Name: ADAM15 RNA Type: mRNA Chromosome: chr1 Starnd: + Coordinate: Start Site(bp): 155050566 End Site(bp): 155062775 External Links: ENSG00000143537

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 NNT chr5 43602692 43707405 + PCSK1N chrX 48831096 48835610 - RBM26 chr13 79311824 79406477 - AC096887.1 chr3 52969119 53099453 - DSG2 chr18 31498177 31549008 + NR3C1 chr5 143277931 143435512 - SF3A2 chr19 2236824 2248655 + MKI67 chr10 128096659 128126423 - HDHD5 chr22 17137511 17165287 - VAMP7 chrX 155881345 155943769 + CBFB chr16 67028984 67101058 + DYNLL2 chr17 58083419 58095542 + KIFC1 chr6 33391823 33409896 + SIGMAR1 chr9 34634722 34637809 - MTRNR2L12 chr3 96617188 96618236 - CNOT9 chr2 218568580 218597080 + OTUD4 chr4 145110838 145180589 - ATG4B chr2 241637213 241673857 + WNK1 chr12 752579 911452 + LTBP1 chr2 32946953 33399509 + MTHFD1 chr14 64388031 64463457 + ALDOA chr16 30064164 30070457 + APEX1 chr14 20455191 20457772 + TNRC18 chr7 5306790 5425414 - HK1 chr10 69269984 69401884 + MARCKS chr6 113857345 113863475 + SETD6 chr16 58515479 58521181 + PAX9 chr14 36657568 36679362 + NEK6 chr9 124257606 124353307 + PCYOX1L chr5 149358037 149369653 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand XIST chrX 73820649 73852723 - 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.