exRNAdisease

Entry Detail

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General Information

Database ID: exR0000453 RNA Name: AKNA RNA Type: mRNA Chromosome: chr9 Starnd: - Coordinate: Start Site(bp): 114334156 End Site(bp): 114394405 External Links: ENSG00000106948

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 TNFAIP3 chr6 137867214 137883312 + RASGRP3 chr2 33436324 33564750 + SSR4 chrX 153793516 153798499 + RPS9 chr19 54200809 54249003 + RPS19 chr19 41860255 41872925 + ATP6V1D chr14 67294371 67360265 - UBALD2 chr17 76265348 76271298 + NDUFS4 chr5 53560633 53683338 + BRMS1 chr11 66337333 66345125 - ETFB chr19 51345169 51366418 - SKP1 chr5 134148935 134177038 - RPL11 chr1 23691742 23696835 + ABCC5 chr3 183919934 184017939 - MLST8 chr16 2204248 2209453 + RPL13 chr16 89560657 89566828 + PGRMC2 chr4 128269237 128288829 - HIKESHI chr11 86302211 86345943 + EIF4B chr12 53006158 53042209 + ERI2 chr16 20780193 20900349 - BUB3 chr10 123154402 123170467 + SHC1 chr1 154962298 154974395 - GLRX3 chr10 130136391 130184521 + HLA-DRB1 chr6 32578769 32589848 - FKBP8 chr19 18531751 18544077 - ALAS1 chr3 52198086 52214327 + TUBB chr6 30720352 30725426 + ATPAF1 chr1 46632737 46673867 - HNRNPA2B1 chr7 26173057 26201529 - PYGO2 chr1 154957026 154963853 - COX7A2L chr2 42333546 42425088 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AL138895.1 chr9 114396724 114398503 - LINC00882 chr3 106449775 107240671 - MIR663AHG chr20 26167817 26251546 - 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.