exRNAdisease

Entry Detail

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General Information

Database ID: exR0000210 RNA Name: ACTR8 RNA Type: mRNA Chromosome: chr3 Starnd: - Coordinate: Start Site(bp): 53867066 End Site(bp): 53882152 External Links: ENSG00000113812

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 + ZDHHC4 chr7 6577434 6589374 + UTP6 chr17 31860904 31901708 - VMP1 chr17 59707192 59842255 + XPO5 chr6 43522334 43576038 - WFS1 chr4 6269849 6303265 + MT-ATP6 chrMT 8527 9207 + FTL chr19 48965309 48966879 + CHPT1 chr12 101696947 101744140 + EDARADD chr1 236348257 236502915 + PAICS chr4 56435741 56464579 + DENND4B chr1 153929501 153946718 - EIF1AX chrX 20124525 20141838 - CLTB chr5 176392455 176416569 - HLA-E chr6 30489509 30494194 + LSM12 chr17 44034328 44067619 - IGF2BP1 chr17 48997385 49056145 + TRAP1 chr16 3651639 3717553 - CD81 chr11 2376177 2397419 + OAZ1 chr19 2269509 2273490 + QPRT chr16 29663279 29698699 + MYO9B chr19 17075781 17214537 + DCAF15 chr19 13952492 13961449 + HLA-B chr6 31269491 31357188 - ACTN4 chr19 38647649 38731589 + RALGPS2 chr1 178725147 178921841 + STRBP chr9 123109500 123268586 - ENO2 chr12 6913745 6923698 + PCYT1B chrX 24558087 24672677 - CTNND1 chr11 57753243 57819546 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC012313.3 chr19 58346854 58362751 - LINC00294 chr11 33076149 33079454 + 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.