exRNAdisease

Entry Detail

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General Information

Database ID: exR0000008 RNA Name: AACS RNA Type: mRNA Chromosome: chr12 Starnd: + Coordinate: Start Site(bp): 125065434 End Site(bp): 125143333 External Links: ENSG00000081760

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 NPM3 chr10 101781325 101783413 - FGFR2 chr10 121478334 121598458 - PDXK chr21 43719094 43762307 + EXOC6B chr2 72175984 72826041 - SIPA1L2 chr1 232397965 232561558 - NOP14 chr4 2937933 2963406 - ZNF579 chr19 55576774 55580848 - MTERF4 chr2 241072169 241102332 - EIF6 chr20 35278911 35284985 - CITED2 chr6 139371807 139374648 - EME1 chr17 50373220 50381483 + PHLDA1 chr12 76025447 76033932 - RPLP2 chr11 809965 812880 + ZBTB44 chr11 130226677 130314917 - KLHL21 chr1 6590724 6614607 - TMEM259 chr19 1009648 1021179 - RPS5 chr19 58386400 58394806 + PCBP2 chr12 53452102 53481162 + VCP chr9 35056064 35072627 - BRD9 chr5 850291 892801 - TRIM13 chr13 49995888 50020481 + SUPT20H chr13 37009312 37059713 - AIFM2 chr10 70098223 70132934 - AL121753.1 chr20 35267885 35280043 - OST4 chr2 27070472 27071654 - HSP90AB1 chr6 44246166 44253888 + BCKDK chr16 31106107 31112791 + AAMP chr2 218264123 218270257 - SELENOH chr11 57741250 57743554 + BUD31 chr7 99408641 99419616 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC023509.1 chr12 53441741 53467528 + XIST chrX 73820649 73852723 - 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.