exRNAdisease

Entry Detail

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General Information

Database ID: exR0000449 RNA Name: AKAP9 RNA Type: mRNA Chromosome: chr7 Starnd: + Coordinate: Start Site(bp): 91940867 End Site(bp): 92110673 External Links: ENSG00000127914

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 CCDC85C chr14 99500190 99604207 - SFRP1 chr8 41261962 41309473 - YWHAE chr17 1344275 1400222 - RBBP6 chr16 24537693 24572863 + SMARCC1 chr3 47585269 47782106 - PABPC1 chr8 100685816 100722809 - C2orf68 chr2 85605254 85612066 - FKBP4 chr12 2794970 2805423 + KDM5C chrX 53191321 53225422 - RHOA chr3 49359145 49412998 - U2AF1 chr21 43092956 43107587 - PIGQ chr16 566995 584136 + ALDOA chr16 30064164 30070457 + UBE2C chr20 45812576 45816957 + ZDHHC9 chrX 129803288 129843909 - TPT1 chr13 45333471 45341370 - CNPY3 chr6 42929192 42939294 + OXA1L chr14 22766522 22773042 + HMGA2 chr12 65824131 65966295 + UQCC2 chr6 33694293 33711727 - KMT2B chr19 35717973 35738878 + MRPL42 chr12 93467488 93516214 + RPS13 chr11 17074388 17077715 - SALL3 chr18 78980275 79002677 + AUP1 chr2 74526645 74529760 - ILF2 chr1 153661788 153671028 - CBX3 chr7 26201162 26213607 + TUBB chr6 30720352 30725426 + C12orf10 chr12 53299695 53307177 + MEX3D chr19 1554669 1568058 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand Z98883.1 chr16 568837 576257 + 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.