exRNAdisease

Entry Detail

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General Information

Database ID: exR0000379 RNA Name: AGO4 RNA Type: mRNA Chromosome: chr1 Starnd: + Coordinate: Start Site(bp): 35808016 End Site(bp): 35857890 External Links: ENSG00000134698

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 ADAM19 chr5 157395534 157575775 - MT1G chr16 56666731 56668065 - POLD2 chr7 44114681 44124358 - UBXN6 chr19 4444999 4457794 - RPLP2 chr11 809965 812880 + TATDN2 chr3 10248023 10281218 + PTGES2 chr9 128120693 128128462 - VAMP3 chr1 7771296 7781432 + CBFA2T2 chr20 33490075 33650036 + TMEM132A chr11 60924463 60937159 + MT-CO3 chrMT 9207 9990 + TRIM73 chr7 75395063 75410996 + SFPQ chr1 35176378 35193145 - PMEL chr12 55954105 55973317 - RPL37 chr5 40825262 40835222 - GATA2 chr3 128479427 128493201 - PTMA chr2 231706895 231713541 + SRGN chr10 69088103 69104805 + YBX1 chr1 42682418 42703805 + SLC38A2 chr12 46358188 46372773 - HNRNPF chr10 43385617 43409166 - ANKH chr5 14704800 14871778 - AGO3 chr1 35930718 36072500 + OSBPL8 chr12 76351797 76559809 - DDX5 chr17 64498254 64508199 - SDF4 chr1 1216908 1232067 - XPO1 chr2 61477849 61538626 - LGMN chr14 92703807 92748679 - ARL8B chr3 5122245 5180912 + GGCT chr7 30496621 30504841 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC124944.3 chr3 195900986 195903417 + NEAT1 chr11 65422774 65445540 + 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.