exRNAdisease

Entry Detail

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General Information

Database ID: exR0000089 RNA Name: ABHD6 RNA Type: mRNA Chromosome: chr3 Starnd: + Coordinate: Start Site(bp): 58237532 End Site(bp): 58295693 External Links: ENSG00000163686

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 AC010422.3 chr19 12643831 12648397 - AMY2B chr1 103553815 103579534 + FSTL1 chr3 120392293 120450993 - GSKIP chr14 96363452 96387288 + HLA-B chr6 31269491 31357188 - NDUFA10 chr2 239892450 240025345 - NME2 chr17 51165435 51171747 + PSMD14 chr2 161308425 161411717 + RPL27A chr11 8682788 8714759 + SLC12A8 chr3 125082636 125212864 - SLC25A29 chr14 100291116 100306547 - SMU1 chr9 33041765 33076674 - SRSF5 chr14 69726900 69772005 + SSBP4 chr19 18418864 18434562 + TERF2IP chr16 75647773 75761872 + TICRR chr15 89575469 89631056 + TMED7 chr5 115613210 115632992 - TPI1 chr12 6867119 6870948 + UBR7 chr14 93207241 93229215 + VIM chr10 17228241 17237593 + WIPF1 chr2 174559572 174682916 - ZFAND2B chr2 219195237 219209651 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC016598.1 chr5 143489855 143531350 - 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.