exRNAdisease

Entry Detail

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General Information

Database ID: exR0000281 RNA Name: ADCK2 RNA Type: mRNA Chromosome: chr7 Starnd: + Coordinate: Start Site(bp): 140672945 End Site(bp): 140696261 External Links: ENSG00000133597

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 TXNIP chr1 145992435 145996579 - RPL13A chr19 49487554 49492308 + RPS25 chr11 119015712 119018691 - RBM47 chr4 40423267 40630875 - INPPL1 chr11 72223701 72239147 + CCAR2 chr8 22604632 22621514 + PLCXD1 chrX 276322 303356 + ITGB2 chr21 44885953 44931989 - NDUFV1 chr11 67605653 67612554 + POGK chr1 166839447 166856344 + MTRNR2L12 chr3 96617188 96618236 - POC1A chr3 52075226 52154690 - HBS1L chr6 134960378 135103056 - RPL27A chr11 8682788 8714759 + RPL35 chr9 124857880 124861981 - NYNRIN chr14 24399003 24419283 + PTMA chr2 231706895 231713541 + TUBA1C chr12 49188736 49274603 + SOX11 chr2 5692384 5701385 + LARP4B chr10 806914 931705 - NDUFB2 chr7 140690777 140722790 + HNRNPA2B1 chr7 26173057 26201529 - RBMX chrX 136848004 136880764 - RPS3 chr11 75399515 75422280 + SPEN chr1 15836095 15940456 + COX10 chr17 14069490 14231736 + ABCA2 chr9 137007234 137028922 - CSE1L chr20 49046246 49096960 + DDHD2 chr8 38225218 38275558 + LSM12 chr17 44034328 44067619 - miRNA targets: NA circRNA targets: NA lncRNA targets: NA 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.