exRNAdisease

Entry Detail

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General Information

Database ID: exR0000156 RNA Name: ACOX1 RNA Type: mRNA Chromosome: chr17 Starnd: - Coordinate: Start Site(bp): 75941507 End Site(bp): 75979177 External Links: ENSG00000161533

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 RPS19 chr19 41860255 41872925 + SAP18 chr13 21140514 21149084 + LAMA3 chr18 23689443 23956222 + ZNF512 chr2 27582969 27623217 + ELAC2 chr17 12991612 13018065 - C3orf52 chr3 112086335 112131004 + MAZ chr16 29806106 29811164 + POU5F1 chr6 31164337 31180731 - ZNF544 chr19 58228594 58277495 + NUP205 chr7 135557917 135648757 + OPA1 chr3 193593144 193697811 + KIF14 chr1 200551497 200620751 - WDR26 chr1 224385143 224437033 - ELF4 chrX 130064874 130110716 - ASXL1 chr20 32358330 32439319 + NRF1 chr7 129611720 129757082 + SMC3 chr10 110567691 110604636 + OSBPL10 chr3 31657890 32077580 - PSAP chr10 71816298 71851325 - TOX4 chr14 21476597 21499175 + PPP6R1 chr19 55229779 55259017 - RPL13A chr19 49487554 49492308 + TNFRSF13B chr17 16929816 16972118 - MREG chr2 215942584 216034096 - NDUFV1 chr11 67605653 67612554 + PPM1G chr2 27381195 27409591 - HLA-A chr6 29941260 29945884 + NOP14 chr4 2937933 2963406 - DCTPP1 chr16 30423615 30430030 - RPL10L chr14 46651010 46651781 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC138761.1 chr17 22266395 22288301 + 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.