exRNAdisease

Entry Detail

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General Information

Database ID: exR0000117 RNA Name: ACADS RNA Type: mRNA Chromosome: chr12 Starnd: + Coordinate: Start Site(bp): 120725774 End Site(bp): 120740008 External Links: ENSG00000122971

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 AC004832.3 chr22 30409255 30428990 + AP002990.1 chr11 62559603 62591531 - CD52 chr1 26317958 26320523 + CHD4 chr12 6570082 6614524 - CYSTM1 chr5 140175156 140282052 + DNAJC5 chr20 63895126 63936031 + EEF1G chr11 62559596 62574086 - EIF2B1 chr12 123620406 123633766 - EIF3J chr15 44537125 44563029 + EIF5AL1 chr10 79512601 79516440 + GPAT2 chr2 96021946 96039451 - HNRNPA2B1 chr7 26173057 26201529 - IMP3 chr15 75639085 75648706 - LRRK1 chr15 100919327 101078257 + MCM7 chr7 100092728 100101940 - MLH1 chr3 36993350 37050846 + MTFP1 chr22 30425623 30429054 + PFKL chr21 44300051 44327376 + PIP4K2C chr12 57591174 57603418 + PPP2R1A chr19 52190048 52229518 + RPLP1 chr15 69452814 69456205 + RPS3 chr11 75399515 75422280 + SMAD7 chr18 48919853 48952052 - STIM1 chr11 3854527 4093210 + TBX3 chr12 114670255 114684175 - TPI1 chr12 6867119 6870948 + TUBB chr6 30720352 30725426 + UNC119B chr12 120710458 120723640 + VCP chr9 35056064 35072627 - 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.