exRNAdisease

Entry Detail

---



General Information

Database ID: exR0000217 RNA Name: ACVR2B RNA Type: mRNA Chromosome: chr3 Starnd: + Coordinate: Start Site(bp): 38453890 End Site(bp): 38493142 External Links: ENSG00000114739

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 SF3A3 chr1 37956975 37990075 - LSM4 chr19 18306230 18323274 - DDX17 chr22 38483438 38507660 - MTCH1 chr6 36968141 36986298 - BCL6 chr3 187721377 187745725 - TCOF1 chr5 150357629 150400308 + LZTS2 chr10 100996618 101007836 + PACSIN2 chr22 42835412 43015149 - CBY1 chr22 38656636 38673854 + ZDBF2 chr2 206274663 206314427 + UNC45A chr15 90930180 90954093 + FAM111B chr11 59107185 59127412 + UBE3B chr12 109477402 109536705 + DNAAF2 chr14 49625174 49635230 - GPAM chr10 112149865 112215377 - CHRFAM7A chr15 30357766 30393849 - SORD chr15 45023181 45077185 + HSPA5 chr9 125234853 125241343 - MT-CO3 chrMT 9207 9990 + TBC1D15 chr12 71839707 71927248 + MYO7A chr11 77128246 77215241 + TUBA1B chr12 49127782 49131397 - HNRNPAB chr5 178204533 178211163 + MRPL12 chr17 81703367 81707517 + SNRPN chr15 24823637 24978723 + AL138752.2 chr9 37588413 38068687 - NT5DC2 chr3 52524385 52535054 - ISOC1 chr5 129094749 129114028 + SLC25A17 chr22 40769630 40819399 - CRMP1 chr4 5748084 5893086 - miRNA targets: miRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand hsa-miR-221-3p chrX 45746180 45746202 - hsa-miR-423-5p chr17 30117095 30117117 + circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC090948.2 chr3 16339308 16339871 + AD000090.1 chr19 35557956 35581954 + LINC01578 chr15 92819540 92899701 + LINC02035 chr3 122886941 122892416 + NEAT1 chr11 65422774 65445540 + XIST chrX 73820649 73852723 - 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.