exRNAdisease

Entry Detail

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General Information

Database ID: exR0000131 RNA Name: ACD RNA Type: mRNA Chromosome: chr16 Starnd: - Coordinate: Start Site(bp): 67657512 End Site(bp): 67660815 External Links: ENSG00000102977

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 DHX9 chr1 182839347 182887982 + DGCR2 chr22 19036282 19122454 - HSP90AB1 chr6 44246166 44253888 + AP002990.1 chr11 62559603 62591531 - ZNF23 chr16 71447597 71463095 - DUSP3 chr17 43766125 43778977 - EEF1G chr11 62559596 62574086 - SEC22C chr3 42547969 42601080 - SLC35B2 chr6 44254096 44257890 - PPM1A chr14 60245752 60299087 + CDK16 chrX 47217860 47229997 + MEPCE chr7 100428790 100434118 + FGFRL1 chr4 1009936 1026898 + NAA10 chrX 153929225 153935080 - MT-CO1 chrMT 5904 7445 + ATP6V1D chr14 67294371 67360265 - EFTUD2 chr17 44849948 44899445 - TFAM chr10 58385345 58399220 + RAF1 chr3 12583601 12664226 - MARCKSL1 chr1 32333839 32336233 - CNOT1 chr16 58519951 58629885 - FSTL3 chr19 676392 683392 + HNRNPD chr4 82352498 82374503 - PCBP2 chr12 53452102 53481162 + TSPAN9 chr12 3077355 3286564 + PSMA4 chr15 78540405 78552417 + GCN1 chr12 120127202 120194715 - COX14 chr12 50112082 50120457 + GNAS chr20 58839718 58911192 + RPS6KA1 chr1 26529761 26575030 + miRNA targets: NA 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.