exRNAdisease

Entry Detail

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General Information

Database ID: exR0000191 RNA Name: ACTL6A RNA Type: mRNA Chromosome: chr3 Starnd: + Coordinate: Start Site(bp): 179562886 End Site(bp): 179588407 External Links: ENSG00000136518

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 RNF167 chr17 4940008 4945222 + FIGN chr2 163593396 163736012 - NPTX2 chr7 98617285 98629869 + ASGR1 chr17 7173431 7179564 - SIX4 chr14 60709539 60724351 - RUFY1 chr5 179550554 179610012 + PABPC1 chr8 100685816 100722809 - AC015813.2 chr17 57989038 58007246 - EEF2 chr19 3976056 3985463 - AC084337.2 chr11 6481485 6508978 + PRPF8 chr17 1650629 1684867 - MT-ND1 chrMT 3307 4262 + CALM1 chr14 90396502 90408268 + INTS6 chr13 51354077 51454264 - HSPA5 chr9 125234853 125241343 - RPL38 chr17 74203582 74210655 + TUBB chr6 30720352 30725426 + GATA2 chr3 128479427 128493201 - ALPL chr1 21509397 21578410 + KMT2A chr11 118436490 118526832 + RHOA chr3 49359145 49412998 - GHITM chr10 84139509 84153568 + MT-CO3 chrMT 9207 9990 + RPS16 chr19 39433137 39435949 - NRBP1 chr2 27427790 27442259 + OAZ1 chr19 2269509 2273490 + B3GNT2 chr2 62196115 62224731 + YPEL3 chr16 30092314 30096915 - JAKMIP1 chr4 6026199 6200591 - WDYHV1 chr8 123416726 123470028 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand ARMCX5-GPRASP2 chrX 102599512 102714671 + RMRP chr9 35657751 35658018 - 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.