exRNAdisease

Entry Detail

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General Information

Database ID: exR0016278 RNA Name: YBX1 RNA Type: mRNA Chromosome: chr1 Starnd: + Coordinate: Start Site(bp): 42682418 End Site(bp): 42703805 External Links: ENSG00000065978

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 ABL1 chr9 130713016 130887675 + ABR chr17 1003518 1229738 - AC008764.4 chr19 16577642 16660115 - AC010422.3 chr19 12643831 12648397 - AC092143.1 chr16 89919165 89936092 + AC118553.2 chr1 99970011 100083321 + AC120057.2 chr17 7240427 7244635 - AC138811.2 chr16 18788063 18801519 - ACAD8 chr11 134253495 134265855 + ACKR3 chr2 236567787 236582354 + ACTB chr7 5527148 5563784 - ACTG1 chr17 81509971 81523847 - ADAM11 chr17 44758988 44781846 + ADD2 chr2 70607618 70768225 - ADGRL2 chr1 81306160 81992436 + AEBP2 chr12 19404045 19720801 + AEN chr15 88621337 88632281 + AFG3L2 chr18 12328944 12377227 - AGL chr1 99850361 99924023 + AGO3 chr1 35930718 36072500 + AGO4 chr1 35808016 35857890 + AKR1E2 chr10 4786629 4848062 + AKT1 chr14 104769349 104795751 - AL136454.1 chr1 192716132 192716653 + AL928654.3 chr14 105487199 105492267 + ALDH9A1 chr1 165662216 165698863 - ALDOA chr16 30064164 30070457 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC016876.2 chr17 7581964 7584086 - AC018521.1 chr17 47945424 47981736 + AC245014.3 chr1 145281116 145281462 + AL031320.2 chr6 143484979 143507327 + AL121992.1 chr1 15586136 15603626 - 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.