exRNAdisease

Entry Detail

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General Information

Database ID: exR0000199 RNA Name: ACTN3 RNA Type: mRNA Chromosome: chr11 Starnd: + Coordinate: Start Site(bp): 66546395 End Site(bp): 66563334 External Links: ENSG00000248746

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 - ACTN1 chr14 68874143 68979440 - ACTN4 chr19 38647649 38731589 + AKT2 chr19 40230317 40285536 - ATG101 chr12 52069246 52077494 + BCAR3 chr1 93561741 93847150 - C19orf48 chr19 50797704 50804929 - CDK18 chr1 205504595 205532793 + CIAO1 chr2 96266159 96274173 + CIRBP chr19 1259384 1274880 + GNAI1 chr7 79768028 80226181 + LPCAT3 chr12 6976185 7018477 - MCM7 chr7 100092728 100101940 - MGST3 chr1 165631213 165661796 + MON1B chr16 77190835 77202398 + NDUFA4 chr7 10931943 10940153 - ODC1 chr2 10439968 10448327 - PDGFA chr7 497258 520296 - PDZD4 chrX 153802166 153830565 - PTTG1IP chr21 44849585 44873903 - RPL27A chr11 8682788 8714759 + SBF2 chr11 9778667 10294207 - SFRP1 chr8 41261962 41309473 - SRCAP chr16 30698209 30741409 + SZRD1 chr1 16352575 16398145 + TIMM29 chr19 10928811 10933535 + VAT1 chr17 43014607 43025123 - VPS35 chr16 46656132 46689518 - WIPF3 chr7 29806486 29917066 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand LINC00847 chr5 180830326 180839742 + 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.