exRNAdisease

Entry Detail

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General Information

Database ID: exR0000149 RNA Name: ACOT13 RNA Type: mRNA Chromosome: chr6 Starnd: + Coordinate: Start Site(bp): 24667035 End Site(bp): 24705065 External Links: ENSG00000112304

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 CCT3 chr1 156308968 156367873 - CDC26 chr9 113255835 113275572 - PARP1 chr1 226360691 226408093 - MTRNR2L8 chr11 10507894 10509186 - NDRG4 chr16 58462846 58513628 + TMEM97 chr17 28319200 28328685 + CBX5 chr12 54230942 54280133 - RAF1 chr3 12583601 12664226 - ZBTB25 chr14 64449106 64505213 - SLC16A3 chr17 82228397 82261129 + FUT4 chr11 94543840 94549898 + TRIM69 chr15 44728988 44767829 + RPS15 chr19 1438358 1440494 + HNRNPUL2-BSCL2 chr11 62690275 62727384 - RPRD1A chr18 35984387 36067576 - EEF1A1 chr6 73515750 73523797 - HNRNPUL2 chr11 62712630 62727457 - AL121594.1 chr14 35122549 35317474 + PRPF38A chr1 52404602 52420836 + FZD3 chr8 28494205 28574267 + SMPDL3A chr6 122789049 122809720 + CALM3 chr19 46601074 46610782 + EFNA1 chr1 155127876 155134899 + EI24 chr11 125569280 125584684 + RND2 chr17 43025231 43032041 + TAF15 chr17 35713791 35864615 + PRRC1 chr5 127517609 127555089 + KDM1A chr1 23019443 23083689 + MSC chr8 71841549 71844468 - MFSD5 chr12 53251251 53254405 + miRNA targets: miRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand hsa-miR-92a-3p chrX 134169544 134169565 - circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand MIR17HG chr13 91347820 91354579 + 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.