exRNAdisease

Entry Detail

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General Information

Database ID: exR0009751 RNA Name: NT5DC2 RNA Type: mRNA Chromosome: chr3 Starnd: - Coordinate: Start Site(bp): 52524385 End Site(bp): 52535054 External Links: ENSG00000168268

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 AAMP chr2 218264123 218270257 - AC002985.1 chr19 18907013 18934397 - AC005324.3 chr17 15571491 15651653 - AC009133.6 chr16 29812261 29820092 + AC087289.3 chr17 75898645 75930129 - ACLY chr17 41866917 41930542 - ACVR2B chr3 38453890 38493142 + ADA2 chr22 17178790 17258235 - ADAT1 chr16 75596981 75623300 - ADRM1 chr20 62302093 62308862 + AGTPBP1 chr9 85546539 85742029 - AHCY chr20 34280268 34311802 - AL589666.1 chr6 85557978 85615234 - AL713999.1 chr1 155169409 155187272 - miRNA targets: miRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand hsa-miR-423-5p chr17 30117095 30117117 + hsa-miR-1286 chr22 20249145 20249165 - circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC016876.2 chr17 7581964 7584086 - AC019205.1 chr6 73263212 73301789 + AC026362.1 chr12 122975320 122982907 + 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.