exRNAdisease

Entry Detail

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General Information

Database ID: exR0000377 RNA Name: AGO2 RNA Type: mRNA Chromosome: chr8 Starnd: - Coordinate: Start Site(bp): 140520156 End Site(bp): 140635633 External Links: ENSG00000123908

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 RPL13 chr16 89560657 89566828 + SPECC1 chr17 20009344 20319026 + ENO1 chr1 8861000 8879190 - EIF2AK1 chr7 6022247 6059175 - RAB5B chr12 55973913 55996683 + PLXNB2 chr22 50274979 50307646 - LENG8 chr19 54448887 54462037 + HNRNPU chr1 244840638 244864560 - SMAD7 chr18 48919853 48952052 - BRIX1 chr5 34915677 34925996 + CD3EAP chr19 45406209 45410766 + PSMC3IP chr17 42572315 42577831 - CCDC137 chr17 81666737 81673904 + TSPYL1 chr6 116267760 116279903 - TIAL1 chr10 119571802 119597029 - AGO1 chr1 35869808 35930532 + GID8 chr20 62938147 62948475 + ERBB2 chr17 39687914 39730426 + TSPAN13 chr7 16753755 16784536 + RMDN3 chr15 40735884 40755851 - TFDP1 chr13 113584721 113641473 + PLXNA1 chr3 126988594 127037392 + PDLIM1 chr10 95237572 95291012 - MCC chr5 113022099 113488823 - RANBP9 chr6 13621498 13711835 - NPC1 chr18 23506184 23586506 - ILF3 chr19 10654261 10692417 + APRT chr16 88809339 88811937 - SMARCD2 chr17 63832081 63843065 - TCF4 chr18 55222185 55664787 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC068831.7 chr15 91022766 91023200 + 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.