exRNAdisease

Entry Detail

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General Information

Database ID: exR0000061 RNA Name: ABCE1 RNA Type: mRNA Chromosome: chr4 Starnd: + Coordinate: Start Site(bp): 145098288 End Site(bp): 145129524 External Links: ENSG00000164163

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 MGST1 chr12 16347142 16609259 + MTX2 chr2 176269395 176338025 + RPL37A chr2 216498825 216579180 + FAM162A chr3 122384176 122412334 + ENOPH1 chr4 82430590 82461177 + ANKRD17 chr4 73073376 73258798 - SLC25A29 chr14 100291116 100306547 - INSIG1 chr7 155297776 155310235 + LAMTOR1 chr11 72085895 72103297 - GNB5 chr15 52115105 52191369 - IVNS1ABP chr1 185296388 185317273 - TIMMDC1 chr3 119498547 119525090 + HOXA3 chr7 27106184 27152581 - STMN1 chr1 25884181 25906991 - UGP2 chr2 63840940 63891562 + RPL3 chr22 39312882 39320389 - PGK1 chrX 77910739 78129295 + RBL2 chr16 53433977 53491648 + BCAT1 chr12 24810024 24949101 - RPS23 chr5 82273320 82278396 - TNPO2 chr19 12699194 12724011 - TUBB chr6 30720352 30725426 + CHTF8 chr16 69118010 69132578 - CLPTM1L chr5 1317752 1345099 - RAB10 chr2 26034084 26137454 + MDH2 chr7 76048051 76067508 + CREBZF chr11 85659708 85682908 - C19orf48 chr19 50797704 50804929 - EWSR1 chr22 29268009 29300525 + ATP5MG chr11 118401606 118431496 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AL157871.6 chr14 100279959 100291456 - FAM215B chr17 46558830 46562795 - MAPKAPK5-AS1 chr12 111839764 111842902 - 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.