exRNAdisease

Entry Detail

---



General Information

Database ID: exR0000161 RNA Name: ACP5 RNA Type: mRNA Chromosome: chr19 Starnd: - Coordinate: Start Site(bp): 11574660 End Site(bp): 11579008 External Links: ENSG00000102575

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 ACTG1 chr17 81509971 81523847 - AL669918.1 chr6 32813767 32838822 - ATP5F1D chr19 1241746 1244825 + B2M chr15 44711487 44718877 + CCT3 chr1 156308968 156367873 - CD226 chr18 69831158 69961803 - COX4I1 chr16 85798633 85807068 + COX6C chr8 99873200 99893707 - ENO1 chr1 8861000 8879190 - GALNT6 chr12 51351247 51392867 - HLA-B chr6 31269491 31357188 - IRAK1 chrX 154010506 154019902 - LTA chr6 31572054 31574324 + NCAPD2 chr12 6493356 6531955 + NME3 chr16 1770286 1771730 - PFN1 chr17 4945652 4949061 - PPP4R3B chr2 55547292 55618880 - PRR7 chr5 177446445 177456286 + RBM33 chr7 155644451 155781485 + RNASET2 chr6 166929504 166957191 - RPL4 chr15 66498015 66524532 - SLC25A6 chrX 1386152 1392113 - SMAD2 chr18 47808957 47931146 - SNRNP40 chr1 31259568 31296788 - TAP2 chr6 32821833 32838770 - TERF2IP chr16 75647773 75761872 + UBC chr12 124911604 124917368 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand SNHG16 chr17 76557764 76565348 + 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.