exRNAdisease

Entry Detail

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General Information

Database ID: exR0000726 RNA Name: AP2M1 RNA Type: mRNA Chromosome: chr3 Starnd: + Coordinate: Start Site(bp): 184174689 End Site(bp): 184184091 External Links: ENSG00000161203

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 AC010422.3 chr19 12643831 12648397 - AC011448.1 chr19 19516227 19536076 + AC087289.3 chr17 75898645 75930129 - ACTB chr7 5527148 5563784 - ACTG1 chr17 81509971 81523847 - ACTR1A chr10 102461881 102502712 - ACVR2B chr3 38453890 38493142 + ADGRG1 chr16 57610652 57665580 + AGBL2 chr11 47659591 47715389 - AGBL5 chr2 27042364 27070622 + AGPS chr2 177392757 177559299 + AIP chr11 67483026 67491103 + AK4 chr1 65147549 65232145 + AKIRIN2 chr6 87674860 87702233 - AKT1 chr14 104769349 104795751 - AL133352.1 chr10 100505628 100529881 - AL136454.1 chr1 192716132 192716653 + miRNA targets: miRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand hsa-miR-3652 chr12 103930425 103930442 + circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC005899.4 chr17 32328441 32329395 + AC006141.1 chr17 51249579 51251748 - AC079781.5 chr7 97851688 97972985 - AC092490.1 chr12 8788253 8795789 + AC099329.1 chr3 42785087 42852428 - AGAP1-IT1 chr2 235505751 235507566 + 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.