exRNAdisease

Entry Detail

---



General Information

Database ID: exR0000472 RNA Name: ALAS1 RNA Type: mRNA Chromosome: chr3 Starnd: + Coordinate: Start Site(bp): 52198086 End Site(bp): 52214327 External Links: ENSG00000023330

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 RAB28 chr4 13361354 13484365 - SUPT6H chr17 28662198 28702679 + ENTPD1 chr10 95711779 95877266 + SELENOH chr11 57741250 57743554 + RBM15B chr3 51391285 51397908 + AGO4 chr1 35808016 35857890 + STIP1 chr11 64185272 64204543 + RAB11B chr19 8389981 8404434 + RBP1 chr3 139517434 139539829 - ATP5MG chr11 118401606 118431496 + RPS29 chr14 49570984 49599164 - MRPL4 chr19 10251901 10260055 + AP2S1 chr19 46838136 46850992 - RPL7 chr8 73290242 73295789 - RPL23 chr17 38847860 38853764 - NR3C1 chr5 143277931 143435512 - ABLIM1 chr10 114431113 114768061 - ENO1 chr1 8861000 8879190 - RPL37A chr2 216498825 216579180 + RAB1A chr2 65070696 65130331 - MGST1 chr12 16347142 16609259 + CBX1 chr17 48070052 48101478 - MYL6 chr12 56158161 56163496 + HNRNPA0 chr5 137745651 137754363 - ZNF207 chr17 32350117 32381886 + PPFIBP2 chr11 7513298 7657127 + KLHL23 chr2 169694488 169776989 + PARVB chr22 43999211 44172949 + ARHGEF11 chr1 156934840 157045370 - NDFIP2 chr13 79481124 79556075 + miRNA targets: NA circRNA targets: NA lncRNA targets: NA 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.