exRNAdisease

Entry Detail

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General Information

Database ID: exR0000238 RNA Name: ADAM23 RNA Type: mRNA Chromosome: chr2 Starnd: + Coordinate: Start Site(bp): 206443532 End Site(bp): 206621127 External Links: ENSG00000114948

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 ASCC2 chr22 29788609 29838304 - C10orf82 chr10 116663696 116670264 - C20orf27 chr20 3753508 3768387 - CABP1 chr12 120640552 120667324 + CBL chr11 119206298 119313926 + DDOST chr1 20651767 20661544 - DHRS7B chr17 21123364 21193265 + EIF5A chr17 7306999 7312463 + GMDS chr6 1623806 2245605 - GRINA chr8 143990056 143993415 + HERC2 chr15 28111040 28322172 - HMGB2 chr4 173331376 173334432 - HSP90AB1 chr6 44246166 44253888 + HSP90B1 chr12 103930107 103953645 + IVNS1ABP chr1 185296388 185317273 - MDC1 chr6 30699807 30717447 - NPM1 chr5 171387116 171411137 + PIP4P1 chr14 20457719 20461612 - RPL13 chr16 89560657 89566828 + RPL23 chr17 38847860 38853764 - RRAGA chr9 19049427 19051025 + SLC39A6 chr18 36108531 36129385 - TEKT3 chr17 15303811 15341632 - TMUB2 chr17 44186970 44191929 + USP1 chr1 62436297 62451804 + miRNA targets: NA circRNA targets: NA lncRNA targets: NA 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.