exRNAdisease

Entry Detail

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General Information

Database ID: exR0000018 RNA Name: AARS2 RNA Type: mRNA Chromosome: chr6 Starnd: - Coordinate: Start Site(bp): 44298731 End Site(bp): 44313347 External Links: ENSG00000124608

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 COX5A chr15 74919791 74938083 - HSP90AB1 chr6 44246166 44253888 + DENND5A chr11 9138825 9265350 - SFT2D3 chr2 127701497 127705242 + USP22 chr17 20999596 21043760 - SRSF5 chr14 69726900 69772005 + FAM83D chr20 38926312 38953106 + RRP12 chr10 97356358 97426076 - WDR27 chr6 169457212 169702067 - KPNB1 chr17 47649476 47685505 + RAD23A chr19 12945855 12953642 + RBM8A chr1 145917714 145927678 - TIMELESS chr12 56416363 56449426 - MIDN chr19 1248553 1259140 + MT-ND2 chrMT 4470 5511 + GRAMD1A chr19 34994784 35026471 + TM9SF3 chr10 96518110 96587452 - TP53I11 chr11 44885903 44951306 - HSP90B1 chr12 103930107 103953645 + NDFIP1 chr5 142108779 142154440 + USP35 chr11 78188812 78215232 + RPL13 chr16 89560657 89566828 + EIF3C chr16 28688558 28735730 + DPPA4 chr3 109326141 109337572 - ARSA chr22 50622754 50628173 - TBL1XR1 chr3 177019340 177228000 - WDR74 chr11 62832342 62841809 - ORAI3 chr16 30949068 30956461 + PTOV1 chr19 49850735 49860744 + PML chr15 73994673 74047827 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC102953.2 chr7 1464497 1467522 - AL355075.4 chr14 20343048 20343685 - EBLN3P chr9 37079645 37090928 + 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.