exRNAdisease

Entry Detail

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General Information

Database ID: exR0000113 RNA Name: ACAD8 RNA Type: mRNA Chromosome: chr11 Starnd: + Coordinate: Start Site(bp): 134253495 End Site(bp): 134265855 External Links: ENSG00000151498

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 CALR chr19 12938578 12944489 + PPA1 chr10 70202835 70233911 - YBX1 chr1 42682418 42703805 + COMMD1 chr2 61888724 62147247 + DCTD chr4 182890060 182917936 - NCK1 chr3 136862208 136951606 + SOS1 chr2 38981549 39124345 - MT-CO3 chrMT 9207 9990 + GSTP1 chr11 67583742 67586656 + PTPRCAP chr11 67435510 67437682 - GTF2A2 chr15 59638062 59657541 - ZNF585B chr19 37181579 37218153 - PGM2 chr4 37826660 37862937 + TBC1D2B chr15 77984036 78077724 - RPS27A chr2 55231903 55235853 + SMARCB1 chr22 23786931 23838008 + MZT2A chr2 131464900 131492743 - CORO1B chr11 67435510 67443821 - SEC62 chr3 169966635 169998373 + TRIM71 chr3 32817997 32897824 + PSMD9 chr12 121888732 121918297 + CCDC86 chr11 60842113 60851081 + PBX1 chr1 164555584 164899296 + VPS26B chr11 134224671 134247788 + ATRAID chr2 27212027 27217178 + EEF1G chr11 62559596 62574086 - PODXL chr7 131500262 131558217 - RPL29 chr3 51993522 51995895 - ISG15 chr1 1001138 1014540 + PDP1 chr8 93857807 93926068 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand BOLA3-AS1 chr2 74148007 74151952 + 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.