exRNAdisease

Entry Detail

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General Information

Database ID: exR0000431 RNA Name: AK6 RNA Type: mRNA Chromosome: chr5 Starnd: - Coordinate: Start Site(bp): 69350984 End Site(bp): 69370013 External Links: ENSG00000085231

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 AL513165.2 chr9 37512547 37592469 - BICC1 chr10 58512872 58831435 + FBXO10 chr9 37510892 37576380 - FOXP4 chr6 41546426 41602384 + GLRX3 chr10 130136391 130184521 + KPNA1 chr3 122421902 122514945 - LTV1 chr6 143843338 143863812 + NFS1 chr20 35668052 35699355 - PPP2R1B chr11 111726908 111766389 - RAB12 chr18 8609437 8639382 + RAB1A chr2 65070696 65130331 - RANBP9 chr6 13621498 13711835 - RBMX chrX 136848004 136880764 - SNRPD2 chr19 45687454 45692569 - TAF9 chr5 69364743 69370013 - TJP1 chr15 29699367 29968865 - USP1 chr1 62436297 62451804 + WDFY4 chr10 48684876 48982956 + WDR7 chr18 56651343 57036606 + ZFAND5 chr9 72351413 72365235 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AD000090.1 chr19 35557956 35581954 + AL138689.2 chr13 106491147 106521630 + IQCH-AS1 chr15 67290636 67521844 - SNHG3 chr1 28505980 28510892 + WDR7-OT1 chr18 57027832 57038845 + 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.