exRNAdisease

Entry Detail

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General Information

Database ID: exR0000468 RNA Name: AKT2 RNA Type: mRNA Chromosome: chr19 Starnd: - Coordinate: Start Site(bp): 40230317 End Site(bp): 40285536 External Links: ENSG00000105221

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 SHC1 chr1 154962298 154974395 - COLGALT1 chr19 17555649 17583162 + UNC13B chr9 35161992 35405338 + SERTAD2 chr2 64631621 64751005 - CIC chr19 42268537 42295797 + ZNF100 chr19 21722771 21767579 - TSPAN3 chr15 77041404 77083984 - CIT chr12 119685791 119877320 - TTLL4 chr2 218710835 218755416 + AL589666.1 chr6 85557978 85615234 - NFAT5 chr16 69565094 69704666 + GSK3A chr19 42230190 42242625 - SMG5 chr1 156249224 156282825 - PCBP4 chr3 51957454 51974016 - TFAP4 chr16 4257186 4273075 - SNX12 chrX 71056332 71073426 - SCAF1 chr19 49642209 49658642 + ACTG1 chr17 81509971 81523847 - PRKCE chr2 45651345 46187990 + RPS19 chr19 41860255 41872925 + ZNF317 chr19 9140397 9163424 + UBE2D2 chr5 139526431 139628434 + SPEN chr1 15836095 15940456 + SYNCRIP chr6 85607785 85643792 - NONO chrX 71283192 71301168 + DDX51 chr12 132136594 132144319 - FBXO11 chr2 47789316 47905793 - CFL1 chr11 65823022 65862026 - RGS1 chr1 192575763 192580024 + EEF1G chr11 62559596 62574086 - miRNA targets: miRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand hsa-miR-485-5p chr14 101055427 101055448 + hsa-miR-641 chr19 40282603 40282626 - hsa-miR-650 chr22 22822791 22822811 + hsa-miR-671-5p chr7 151238449 151238471 + hsa-miR-423-5p chr17 30117095 30117117 + hsa-miR-1224-5p chr3 184241405 184241423 + hsa-miR-1294 chr5 154347153 154347174 + circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC007952.4 chr17 19112000 19112636 - AC012321.1 chr16 69703065 69704652 + AC012510.1 chr2 218633256 218634014 - AC020663.1 chr16 4730115 4752565 - AC091564.7 chr11 6610883 6616594 - AC093249.6 chr16 30697707 30699058 - AC109460.3 chr16 28974804 28990775 + AC118344.1 chr19 40273489 40275479 - AD000090.1 chr19 35557956 35581954 + AL355075.4 chr14 20343048 20343685 - AL589642.1 chr9 32633454 32648685 + DANCR chr4 52712404 52720351 + HCG18 chr6 30286690 30327382 - LINC01002 chr19 198264 246544 - NEAT1 chr11 65422774 65445540 + 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.