exRNAdisease

Entry Detail

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General Information

Database ID: exR0000411 RNA Name: AIDA RNA Type: mRNA Chromosome: chr1 Starnd: - Coordinate: Start Site(bp): 222668013 End Site(bp): 222713210 External Links: ENSG00000186063

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 EEF1A1 chr6 73515750 73523797 - RPS6 chr9 19375715 19380236 - SALL1 chr16 51135975 51151367 - PDIA6 chr2 10783391 10837977 - STRN4 chr19 46719511 46746994 - RARRES2 chr7 150338317 150341662 - SH2B2 chr7 102285091 102321711 + TMEM106C chr12 47963569 47968878 + HLA-B chr6 31269491 31357188 - URI1 chr19 29923644 30016612 + PHGDH chr1 119648411 119744226 + UBXN1 chr11 62676498 62679117 - EMD chrX 154379273 154381523 + MRPL13 chr8 120380761 120445402 - SMAD4 chr18 51028394 51085045 + EIF4G1 chr3 184314495 184335358 + FEM1B chr15 68277745 68295862 + RPL4 chr15 66498015 66524532 - RAB8B chr15 63189560 63267776 + RPL11 chr1 23691742 23696835 + PAK1IP1 chr6 10694972 10709782 + MIF chr22 23894383 23895227 + EPB41L5 chr2 120013077 120179119 + ATP2B1 chr12 89588049 89709300 - ZFP36L2 chr2 43222402 43226606 - ADAR chr1 154582057 154628013 - NSMCE1 chr16 27224994 27268772 - GPSM1 chr9 136327476 136359605 + CPNE3 chr8 86514435 86561498 + AHNAK chr11 62433542 62556235 - 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.