exRNAdisease

Entry Detail

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General Information

Database ID: exR0000038 RNA Name: ABCB10 RNA Type: mRNA Chromosome: chr1 Starnd: - Coordinate: Start Site(bp): 229516582 End Site(bp): 229558707 External Links: ENSG00000135776

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 PKN1 chr19 14433053 14471867 + HELQ chr4 83407343 83455855 - MBOAT7 chr19 54173412 54189882 - RPL32 chr3 12834485 12841582 - DUSP16 chr12 12473282 12562863 - CBX6 chr22 38861422 38872249 - FOXK1 chr7 4682295 4771442 + NISCH chr3 52455118 52493068 + MTA1 chr14 105419820 105470729 + METTL9 chr16 21597218 21657473 + ESPL1 chr12 53268299 53293638 + NPHP4 chr1 5862811 5992473 - GAREM1 chr18 32124877 32470882 - RPS3 chr11 75399515 75422280 + NELL2 chr12 44508275 44921848 - VPS13D chr1 12230030 12512047 + BRWD1 chr21 39184176 39321559 - PRELID1 chr5 177303799 177306949 + NAT10 chr11 34105617 34147670 + HTATSF1 chrX 136497079 136512346 + GAN chr16 81314966 81380198 + PUS3 chr11 125893485 125903221 - CLPTM1 chr19 44954585 44993341 + DPP9 chr19 4675224 4724673 - CCZ1 chr7 5898725 5926550 + SLC37A4 chr11 119024114 119030906 - MLEC chr12 120687149 120701859 + BRSK2 chr11 1389899 1462689 + MAP4 chr3 47850690 48089272 - PI4KB chr1 151291797 151327715 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand SNHG4 chr5 139274102 139284899 + 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.