exRNAdisease

Entry Detail

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General Information

Database ID: exR0000228 RNA Name: ADAM11 RNA Type: mRNA Chromosome: chr17 Starnd: + Coordinate: Start Site(bp): 44758988 End Site(bp): 44781846 External Links: ENSG00000073670

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 AGRN chr1 1020120 1056118 + CREBZF chr11 85659708 85682908 - CSDE1 chr1 114716913 114758676 - FANCA chr16 89737549 89816657 - GHDC chr17 42188799 42194532 - GOLPH3 chr5 32124716 32174319 - HCFC1 chrX 153947557 153971818 - HDGFL3 chr15 83112738 83207823 - KIAA1841 chr2 61065871 61138034 + LMNB2 chr19 2427638 2456959 - LRP6 chr12 12116025 12267044 - MCC chr5 113022099 113488823 - MDC1 chr6 30699807 30717447 - MDGA1 chr6 37630679 37699306 - MT-ND1 chrMT 3307 4262 + NISCH chr3 52455118 52493068 + NOP53 chr19 47745546 47757058 + PLXNA1 chr3 126988594 127037392 + SF3B3 chr16 70523791 70577670 + SNX17 chr2 27370496 27377535 + TLE3 chr15 70047790 70098176 - TM9SF2 chr13 99446311 99564048 + TMEM25 chr11 118531041 118547280 + TNPO2 chr19 12699194 12724011 - TUBB chr6 30720352 30725426 + UNC119B chr12 120710458 120723640 + YBX1 chr1 42682418 42703805 + ZNF70 chr22 23738682 23751112 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand LINC02228 chr5 25087450 25190956 - 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.