exRNAdisease

Entry Detail

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General Information

Database ID: exR0000072 RNA Name: ABHD11 RNA Type: mRNA Chromosome: chr7 Starnd: - Coordinate: Start Site(bp): 73736094 End Site(bp): 73738867 External Links: ENSG00000106077

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 ANP32E chr1 150218417 150236156 - APLP1 chr19 35867899 35879791 + CHMP5 chr9 33264879 33282070 + ENO2 chr12 6913745 6923698 + EXOSC9 chr4 121801317 121817021 + GNB1 chr1 1785285 1891117 - ITCH chr20 34363241 34540748 + MED24 chr17 40019097 40061215 - MRPS27 chr5 72219409 72320646 - MTRR chr5 7851186 7906025 + NUP153 chr6 17615035 17706834 - PAN2 chr12 56316223 56334053 - SEC24C chr10 73744372 73772161 + SNRNP70 chr19 49085419 49108605 + USP28 chr11 113797874 113875570 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand NEAT1 chr11 65422774 65445540 + 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.