exRNAdisease

Entry Detail

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General Information

Database ID: exR0000026 RNA Name: ABCA1 RNA Type: mRNA Chromosome: chr9 Starnd: - Coordinate: Start Site(bp): 104781006 End Site(bp): 104928155 External Links: ENSG00000165029

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 COX5B chr2 97646062 97648383 + EIF3L chr22 37848868 37889407 + EWSR1 chr22 29268009 29300525 + FEN1 chr11 61792911 61797238 + GANAB chr11 62624826 62646726 - GAPDH chr12 6534512 6538374 + HADH chr4 107989714 108035175 + IGF2 chr11 2129112 2141238 - IGF2BP3 chr7 23310209 23470491 - KDM3B chr5 138352685 138437028 + LSMEM1 chr7 112480853 112491062 + LUC7L3 chr17 50719565 50756219 + MPI chr15 74890005 74902219 + NISCH chr3 52455118 52493068 + PIANP chr12 6693792 6700800 - PPRC1 chr10 102132994 102150333 + RPL13A chr19 49487554 49492308 + RPL14 chr3 40457292 40468587 + RPL19 chr17 39200283 39204732 + RPS23 chr5 82273320 82278396 - SEC11A chr15 84669538 84716460 - SHROOM3 chr4 76435229 76783253 + SND1 chr7 127652194 128092609 + UBE2R2 chr9 33817160 33920399 + ZNF217 chr20 53567065 53609907 - ZNF568 chr19 36916329 36998700 + ZNF696 chr8 143289676 143299952 + miRNA targets: miRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand hsa-miR-1294 chr5 154347153 154347174 + circRNA targets: NA lncRNA targets: NA 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.