exRNAdisease

Entry Detail

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General Information

Database ID: exR0000881 RNA Name: ARHGDIA RNA Type: mRNA Chromosome: chr17 Starnd: - Coordinate: Start Site(bp): 81867721 End Site(bp): 81871378 External Links: ENSG00000141522

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 ABI2 chr2 203328239 203447728 + AC010132.3 chr7 42909273 42932174 - AC011005.1 chr7 129126518 129130793 + AC018512.1 chr15 43772617 43799133 - AC020909.1 chr19 50415799 50428409 + AC093525.2 chr16 2496032 2520218 + AC120057.2 chr17 7240427 7244635 - ACBD6 chr1 180269653 180502954 - ACER3 chr11 76860867 77026797 + ACTB chr7 5527148 5563784 - ACTG1 chr17 81509971 81523847 - ADAR chr1 154582057 154628013 - ADORA2A chr22 24417879 24442357 + AGRN chr1 1020120 1056118 + AKT1 chr14 104769349 104795751 - AKT1S1 chr19 49869033 49878459 - ALAD chr9 113386312 113401290 - miRNA targets: miRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand hsa-miR-16-5p chr3 160404754 160404775 + hsa-miR-339-5p chr7 1022990 1023012 - hsa-miR-497-5p chr17 7017979 7017999 - hsa-miR-588 chr6 126484646 126484666 + hsa-miR-423-5p chr17 30117095 30117117 + hsa-miR-541-3p chr14 101064548 101064569 + hsa-miR-744-5p chr17 12081909 12081930 + hsa-miR-1321 chrX 85835832 85835849 + circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC007218.1 chr16 9666885 9676843 - AC060780.1 chr17 43148368 43171037 - AC099329.1 chr3 42785087 42852428 - AC109460.3 chr16 28974804 28990775 + AC124068.2 chr15 89335053 89336161 + 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.