exRNAdisease

Entry Detail

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General Information

Database ID: exR0000150 RNA Name: ACOT2 RNA Type: mRNA Chromosome: chr14 Starnd: + Coordinate: Start Site(bp): 73567620 End Site(bp): 73575658 External Links: ENSG00000119673

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 ACOT1 chr14 73537143 73543796 + ACOT4 chr14 73591706 73596496 + ACOT6 chr14 73610945 73619888 + ACSL4 chrX 109624244 109733403 - AL136295.5 chr14 24147548 24166452 + ANKRD16 chr10 5861616 5889906 - CRABP2 chr1 156699606 156705816 - ESYT2 chr7 158730995 158830253 - GOT2 chr16 58707131 58734342 - LIN28A chr1 26410817 26429728 + MRPL4 chr19 10251901 10260055 + MRPS10 chr6 42206807 42217861 - MUC4 chr3 195746765 195811973 - NBN chr8 89933336 90003228 - PARK7 chr1 7954291 7985505 + RNF130 chr5 179911651 180072113 - RNF31 chr14 24146683 24160660 + RPL18 chr19 48615328 48619184 - RPS9 chr19 54200809 54249003 + SDC3 chr1 30869466 30908758 - SDHAF4 chr6 70566917 70589569 + SEMA5B chr3 122909082 123028605 - SIGIRR chr11 405716 417455 - SIVA1 chr14 104753147 104768494 + TARDBP chr1 11012344 11026420 + TMEM259 chr19 1009648 1021179 - TSC22D4 chr7 100463359 100479232 - TTI1 chr20 37983007 38033461 - UBC chr12 124911604 124917368 - 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.