exRNAdisease

Entry Detail

---



General Information

Database ID: exR0000264 RNA Name: ADAMTS7 RNA Type: mRNA Chromosome: chr15 Starnd: - Coordinate: Start Site(bp): 78759206 End Site(bp): 78811464 External Links: ENSG00000136378

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 CCT7 chr2 73233420 73253021 + CHD4 chr12 6570082 6614524 - CMTM3 chr16 66603874 66613892 + EEF2 chr19 3976056 3985463 - ENOPH1 chr4 82430590 82461177 + FADS1 chr11 61799627 61829318 - GNAI2 chr3 50226292 50259362 + HEY1 chr8 79764010 79767857 - HSP90AB1 chr6 44246166 44253888 + LSS chr21 46188141 46228824 - MEIS3 chr19 47403124 47419527 - MORF4L1 chr15 78810487 78898139 + NXN chr17 799310 979776 - OLFML2A chr9 124777133 124814885 + PABPC1 chr8 100685816 100722809 - POU5F1 chr6 31164337 31180731 - PPP1R13L chr19 45379638 45406349 - SMG1 chr16 18804853 18926454 - SNX17 chr2 27370496 27377535 + TPM3 chr1 154155304 154194648 - TRAF7 chr16 2155698 2178129 + WWC2 chr4 183099257 183320777 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand SNHG15 chr7 44983023 44986961 - 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.