exRNAdisease

Entry Detail

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General Information

Database ID: exR0010142 RNA Name: P4HB RNA Type: mRNA Chromosome: chr17 Starnd: - Coordinate: Start Site(bp): 81843161 End Site(bp): 81860624 External Links: ENSG00000185624

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 ABCB7 chrX 75051048 75156732 - ABCF2 chr7 151207837 151227166 - ABLIM1 chr10 114431113 114768061 - ABR chr17 1003518 1229738 - AC010132.3 chr7 42909273 42932174 - AC015813.2 chr17 57989038 58007246 - AC087289.3 chr17 75898645 75930129 - ACAD11 chr3 132558138 132660082 - ACLY chr17 41866917 41930542 - ACOT9 chrX 23701055 23766475 - ACTB chr7 5527148 5563784 - ACTG1 chr17 81509971 81523847 - ACTR3 chr2 113890063 113962596 + ADD2 chr2 70607618 70768225 - ADORA2A chr22 24417879 24442357 + ADPRHL2 chr1 36088892 36093932 + ADSL chr22 40346500 40390463 + AGRN chr1 1020120 1056118 + AHCY chr20 34280268 34311802 - AK2 chr1 33007940 33080996 - AKR1B1 chr7 134442356 134459284 - AKT1 chr14 104769349 104795751 - AL022238.4 chr22 40346529 40410054 + AL121758.1 chr20 646626 675800 - AL590764.2 chrX 71103987 71111575 - ALDH1B1 chr9 38392702 38398661 + ALDOA chr16 30064164 30070457 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC055860.1 chr11 18000542 18022931 - AC060780.1 chr17 43148368 43171037 - AD000090.1 chr19 35557956 35581954 + 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.