exRNAdisease

Entry Detail

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General Information

Database ID: exR0000425 RNA Name: AJUBA RNA Type: mRNA Chromosome: chr14 Starnd: - Coordinate: Start Site(bp): 22971177 End Site(bp): 22982551 External Links: ENSG00000129474

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 RXRA chr9 134317098 134440585 + RACK1 chr5 181236897 181248096 - ARL6IP4 chr12 122980060 122982913 + SORL1 chr11 121452314 121633763 + PISD chr22 31618491 31662432 - LDHA chr11 18394560 18408425 + TUBA1A chr12 49184795 49189080 - B2M chr15 44711487 44718877 + SUGP2 chr19 18990888 19034023 - HNRNPC chr14 21209136 21269494 - AC003006.1 chr19 57682045 57753575 + IFITM3 chr11 319676 327537 - VDAC1 chr5 133971871 134004975 - TPT1 chr13 45333471 45341370 - CACNG8 chr19 53963040 53990215 + HMGA1 chr6 34236873 34246231 + RAVER1 chr19 10316212 10333638 - PSMD10 chrX 108084207 108091549 - CNBP chr3 129169484 129183922 - CAPZA2 chr7 116811070 116922049 + SHMT1 chr17 18327860 18363563 - VPS4A chr16 69311350 69326939 + CMTM6 chr3 32481312 32502852 - GAPDH chr12 6534512 6538374 + ZNF551 chr19 57681969 57717301 + TRNP1 chr1 26993692 27000886 + CPNE1 chr20 35626031 35664956 - RPL13A chr19 49487554 49492308 + HIGD2A chr5 176388751 176389761 + DDB1 chr11 61299451 61342596 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC026362.1 chr12 122975320 122982907 + AC079949.1 chr12 127142029 127146532 - AP003392.4 chr11 119065263 119065677 - 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.