exRNAdisease

Entry Detail

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General Information

Database ID: exR0000155 RNA Name: ACOT9 RNA Type: mRNA Chromosome: chrX Starnd: - Coordinate: Start Site(bp): 23701055 End Site(bp): 23766475 External Links: ENSG00000123130

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 CALM2 chr2 47160083 47176921 - NKX1-2 chr10 124445243 124450035 - PKP3 chr11 392614 404908 + GDI2 chr10 5765223 5842132 - RPLP1 chr15 69452814 69456205 + TTLL3 chr3 9808086 9855138 + KPNA5 chr6 116681187 116741867 + PKN2 chr1 88684222 88836255 + PLEKHB2 chr2 131104847 131353709 + AIP chr11 67483026 67491103 + MT-CO2 chrMT 7586 8269 + NUP155 chr5 37288137 37371106 - PIEZO1 chr16 88715338 88785220 - N4BP2L2 chr13 32432417 32538885 - OCLN chr5 69492292 69558104 + CEP55 chr10 93496612 93529092 + HLA-C chr6 31268749 31272130 - PNPO chr17 47941506 47949308 + MYDGF chr19 4641374 4670362 - SSBP1 chr7 141738334 141787922 + NECAP2 chr1 16440721 16460078 + RPS16 chr19 39433137 39435949 - HMGCS1 chr5 43287470 43313512 - DICER1 chr14 95086228 95158010 - ANKRD46 chr8 100509752 100559784 - PCBP1 chr2 70087477 70089203 + PHTF2 chr7 77798792 77957503 + RGS1 chr1 192575763 192580024 + ADNP chr20 50888916 50931437 - CD74 chr5 150400041 150412929 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand JPX chrX 73944182 74070408 + 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.