exRNAdisease

Entry Detail

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General Information

Database ID: exR0000082 RNA Name: ABHD17A RNA Type: mRNA Chromosome: chr19 Starnd: - Coordinate: Start Site(bp): 1876810 End Site(bp): 1885547 External Links: ENSG00000129968

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 SLC20A2 chr8 42416475 42541926 - PPP4R3A chr14 91457611 91510554 - AP001931.1 chr11 57741779 57804771 + EFNB2 chr13 106489745 106535662 - DNAJB1 chr19 14514769 14529770 - RPS15 chr19 1438358 1440494 + MSH5-SAPCD1 chr6 31740020 31764851 + TUBB2A chr6 3153666 3157544 - NBEAL2 chr3 46979666 47009704 + PRPF6 chr20 63981132 64033100 + PIP5K1C chr19 3630183 3700479 - CEBPG chr19 33373685 33382686 + NAA16 chr13 41311267 41377030 + SUPT5H chr19 39436156 39476670 + MT-CO2 chrMT 7586 8269 + LUC7L2 chr7 139340359 139423457 + AC091167.2 chr15 90249556 90272208 + ELMO2 chr20 46366050 46432985 - HNRNPH1 chr5 179614178 179634784 - ACOT7 chr1 6264269 6394391 - SETD5 chr3 9397615 9479240 + ABHD17C chr15 80679684 80755621 + GPX4 chr19 1103926 1106791 + EIF5 chr14 103333544 103345025 + NUB1 chr7 151341699 151378449 + FGFR1 chr8 38400215 38468834 - NF2 chr22 29603556 29698598 + RBCK1 chr20 407498 430966 + UPF1 chr19 18831938 18868236 + SLC25A3 chr12 98593591 98606379 + 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.