exRNAdisease

Entry Detail

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General Information

Database ID: exR0000126 RNA Name: ACBD3 RNA Type: mRNA Chromosome: chr1 Starnd: - Coordinate: Start Site(bp): 226144679 End Site(bp): 226186741 External Links: ENSG00000182827

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 MTRNR2L12 chr3 96617188 96618236 - SLC16A2 chrX 74421493 74533917 + RPS24 chr10 78033760 78056813 + NUSAP1 chr15 41320794 41381050 + LRWD1 chr7 102464956 102473168 + S1PR4 chr19 3172346 3180332 + RSU1 chr10 16590611 16817463 - RPL15 chr3 23916545 23924374 + FOCAD chr9 20658309 20995955 + GPR176 chr15 39799008 39920266 - RAPGEF1 chr9 131576770 131740074 - UTP18 chr17 51260546 51297936 + LIMCH1 chr4 41359607 41700044 + ZNF224 chr19 44094339 44109886 + TTC39C chr18 23992773 24135610 + IGFBP5 chr2 216672105 216695549 - YTHDF1 chr20 63195429 63216139 - RGS10 chr10 119499817 119542719 - CFL1 chr11 65823022 65862026 - TPT1 chr13 45333471 45341370 - RASGRP2 chr11 64726911 64745456 - ACLY chr17 41866917 41930542 - UQCRQ chr5 132866630 132868847 + ID4 chr6 19837370 19842197 + CSNK1E chr22 38290691 38318084 - PUM1 chr1 30931506 31065991 - ZBTB33 chrX 120250752 120258398 + TSN chr2 121737103 121767853 + HK1 chr10 69269984 69401884 + DNPEP chr2 219373527 219400022 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC009404.1 chr2 117833937 117841658 + AC023908.2 chr15 39770559 39801333 - AL022311.1 chr22 37876148 37895563 + AL513314.2 chr1 222477252 222504622 - MIR663AHG chr20 26167817 26251546 - 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.