exRNAdisease

Entry Detail

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General Information

Database ID: exR0000125 RNA Name: ACAT2 RNA Type: mRNA Chromosome: chr6 Starnd: + Coordinate: Start Site(bp): 159762045 End Site(bp): 159779112 External Links: ENSG00000120437

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 RIMS3 chr1 40620680 40665682 - RPL13 chr16 89560657 89566828 + ATP5MC2 chr12 53632726 53677408 - TTF2 chr1 117060326 117107453 + FAM83F chr22 39994954 40043534 + TMEM14C chr6 10722915 10731129 + PWP2 chr21 44107373 44131181 + CINP chr14 102341102 102362916 - FKBP8 chr19 18531751 18544077 - PFN1 chr17 4945652 4949061 - HDAC11 chr3 13479724 13506424 + RIOX1 chr14 73490933 73493394 + HSF1 chr8 144291591 144314720 + SLC7A3 chrX 70925579 70931125 - RPS13 chr11 17074388 17077715 - ALG12 chr22 49900229 49918438 - SKIL chr3 170357678 170396835 + BTG1 chr12 92140278 92145846 - FDPS chr1 155308748 155320666 + ZCCHC10 chr5 132996985 133026604 - IFT27 chr22 36758202 36776256 - SURF2 chr9 133356550 133361158 + COX6B1 chr19 35648323 35658782 + ZNF451 chr6 57086844 57170305 + RPL30 chr8 98024851 98046469 - MLYCD chr16 83899115 83951445 + HAUS4 chr14 22946228 22957161 - RPL37 chr5 40825262 40835222 - MTRNR2L11 chr1 237943724 237945275 - KDM4A chr1 43650149 43705518 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AD000090.1 chr19 35557956 35581954 + AL158835.3 chr10 125707416 125749525 - HCP5 chr6 31463170 31478936 + PRNCR1 chr8 127079874 127092600 + 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.