exRNAdisease

Entry Detail

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General Information

Database ID: exR0000310 RNA Name: ADIPOR1 RNA Type: mRNA Chromosome: chr1 Starnd: - Coordinate: Start Site(bp): 202940826 End Site(bp): 202958572 External Links: ENSG00000159346

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 HEATR6 chr17 60041008 60078922 - SLC25A3 chr12 98593591 98606379 + CHD8 chr14 21385194 21456126 - PMM2 chr16 8788823 8849325 + ATP6AP1 chrX 154428645 154436516 + MAP3K11 chr11 65597756 65615382 - PLSCR3 chr17 7389727 7394842 - TMED5 chr1 93149742 93180516 - HIVEP1 chr6 12008762 12164999 + HSCB chr22 28742039 28757515 + TMEM109 chr11 60914158 60923443 + PDIA4 chr7 149003062 149028662 - TUBA1B chr12 49127782 49131397 - PCNX3 chr11 65615773 65637439 + CELF1 chr11 47465933 47565569 - PLIN2 chr9 19108375 19149290 - COMMD4 chr15 75336020 75343224 + TMED3 chr15 79311112 79427432 + SC5D chr11 121292681 121313410 + TRAPPC10 chr21 44012309 44106552 + HNRNPH1 chr5 179614178 179634784 - MGAT1 chr5 180784782 180815652 - RBAK chr7 5045821 5069487 + ZC3H18 chr16 88570381 88631966 + AQR chr15 34851782 34969742 - PPIA chr7 44796680 44824564 + DOCK2 chr5 169637268 170083382 + COX7C chr5 86617928 86620962 + MARCKSL1 chr1 32333839 32336233 - NEK3 chr13 52132639 52159861 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC006064.5 chr12 6510275 6510522 + AC010733.2 chr2 60925909 60931610 + AC022167.2 chr16 8848105 8860456 + AC020915.1 chr19 58278966 58315197 + MALAT1 chr11 65497688 65506516 + NORAD chr20 36045618 36051018 - 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.