exRNAdisease

Entry Detail

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General Information

Database ID: exR0000118 RNA Name: ACADSB RNA Type: mRNA Chromosome: chr10 Starnd: + Coordinate: Start Site(bp): 123008979 End Site(bp): 123058290 External Links: ENSG00000196177

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 B2M chr15 44711487 44718877 + B4GAT1 chr11 66345374 66347629 - BUB3 chr10 123154402 123170467 + C11orf58 chr11 16613132 16758340 + CCND2 chr12 4273762 4305353 + COX18 chr4 73052362 73069755 - DDX24 chr14 94048287 94081212 - DHCR24 chr1 54849627 54887195 - EIF4E chr4 98871684 98930637 - HLA-B chr6 31269491 31357188 - MCFD2 chr2 46901870 46941855 - MICB chr6 31494881 31511124 + NCOR1 chr17 16029157 16218185 - NFATC3 chr16 68084751 68229259 + NOP53 chr19 47745546 47757058 + POGK chr1 166839447 166856344 + POLE3 chr9 113407235 113410675 - RFFL chr17 35005990 35089319 - TPT1 chr13 45333471 45341370 - VMP1 chr17 59707192 59842255 + YWHAE chr17 1344275 1400222 - YWHAQ chr2 9583967 9630997 - ZNF100 chr19 21722771 21767579 - 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.