exRNAdisease

Entry Detail

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General Information

Database ID: exR0000172 RNA Name: ACSL3 RNA Type: mRNA Chromosome: chr2 Starnd: + Coordinate: Start Site(bp): 222860942 End Site(bp): 222944639 External Links: ENSG00000123983

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 BCORL1 chrX 129981107 130058083 + GANAB chr11 62624826 62646726 - TMA7 chr3 48440257 48444208 + TPMT chr6 18128311 18155077 - EIF1B chr3 40309707 40312424 + AIFM1 chrX 130129362 130165887 - IRX3 chr16 54283304 54286787 - OTUD1 chr10 23439458 23442390 + VASN chr16 4371848 4383538 + TTC37 chr5 95461755 95555007 - EP300 chr22 41092592 41180077 + NSUN4 chr1 46340177 46365152 + MED1 chr17 39404285 39451272 - MAGT1 chrX 77826364 77895593 - EEF2 chr19 3976056 3985463 - ZWILCH chr15 66504959 66550130 + RPL7L1 chr6 42879616 42889925 + AP001781.2 chr11 111786286 111879425 - RPS7 chr2 3575260 3580920 + TUBA1A chr12 49184795 49189080 - SMARCC1 chr3 47585269 47782106 - DDX39B chr6 31530219 31542448 - IQSEC1 chr3 12897043 13283281 - DBN1 chr5 177456608 177474401 - MRFAP1 chr4 6640091 6642745 + ISCA1 chr9 86264546 86283102 - GNA12 chr7 2728105 2844308 - INTS13 chr12 26905181 26938326 - DMXL2 chr15 51447711 51622833 - CD47 chr3 108043091 108091862 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC010733.2 chr2 60925909 60931610 + AC245033.2 chr15 82540870 82562374 + LINC00836 chr10 25651712 25732935 + 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.