exRNAdisease

Entry Detail

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General Information

Database ID: exR0003727 RNA Name: DDIT4 RNA Type: mRNA Chromosome: chr10 Starnd: + Coordinate: Start Site(bp): 72273924 End Site(bp): 72276036 External Links: ENSG00000168209

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 ABI2 chr2 203328239 203447728 + AC005258.1 chr19 2269525 2341172 + AC006064.6 chr12 6556886 6607367 - AC008982.1 chr19 38817471 38840178 - AC010422.3 chr19 12643831 12648397 - AC011462.1 chr19 41350853 41425001 + AC011511.4 chr19 10315471 10320678 - AC068547.1 chr2 151802651 151973949 - AC092143.1 chr16 89919165 89936092 + AC139530.2 chr17 81703371 81720539 + ACLY chr17 41866917 41930542 - ACTA2 chr10 88935074 88991339 - ACTB chr7 5527148 5563784 - ACTG1 chr17 81509971 81523847 - ACTR1B chr2 97655939 97664044 - ADAMTS12 chr5 33523535 33892019 - ADAR chr1 154582057 154628013 - ADH5 chr4 99070978 99088801 - ADM chr11 10305073 10307397 + ADRM1 chr20 62302093 62308862 + AGFG1 chr2 227472152 227561214 + AHCYL1 chr1 109984765 110023742 + AIFM1 chrX 130129362 130165887 - AK2 chr1 33007940 33080996 - AKNA chr9 114334156 114394405 - miRNA targets: miRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand hsa-miR-221-3p chrX 45746180 45746202 - circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC004771.3 chr17 4967995 4968822 + AC016876.2 chr17 7581964 7584086 - AC020663.1 chr16 4730115 4752565 - AC025165.5 chr12 57803838 57804415 + AC135048.1 chr16 30948386 30956511 + AC234582.1 chr1 155195004 155205495 + AD000090.1 chr19 35557956 35581954 + 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.