exRNAdisease

Entry Detail

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General Information

Database ID: exR0000251 RNA Name: ADAMTS13 RNA Type: mRNA Chromosome: chr9 Starnd: + Coordinate: Start Site(bp): 133414358 End Site(bp): 133459402 External Links: ENSG00000160323

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 ATXN10 chr22 45671798 45845307 + BCR chr22 23179704 23318037 + CCDC124 chr19 17933015 17943991 + DDX24 chr14 94048287 94081212 - EME2 chr16 1772810 1781708 + ESYT1 chr12 56118250 56144671 + GCN1 chr12 120127202 120194715 - GDI2 chr10 5765223 5842132 - GNS chr12 64713445 64759431 - LUC7L chr16 188969 229463 - MAPK9 chr5 180233143 180292099 - MARCKSL1 chr1 32333839 32336233 - NDUFV1 chr11 67605653 67612554 + PDXK chr21 43719094 43762307 + PLEKHJ1 chr19 2230084 2237704 - PPP2R1A chr19 52190048 52229518 + PTOV1 chr19 49850735 49860744 + PTPN11 chr12 112418351 112509913 + SPG11 chr15 44562696 44663678 - SPG7 chr16 89490719 89557768 + SUV39H1 chrX 48695554 48709012 + WDR34 chr9 128633661 128656787 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC121761.1 chr12 75483454 75489820 - AC124068.2 chr15 89335053 89336161 + Z95331.1 chr22 45657019 45680130 + 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.