exRNAdisease

Entry Detail

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General Information

Database ID: exR0000044 RNA Name: ABCB8 RNA Type: mRNA Chromosome: chr7 Starnd: + Coordinate: Start Site(bp): 151028422 End Site(bp): 151047782 External Links: ENSG00000197150

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 USP20 chr9 129834698 129881838 + RANBP1 chr22 20115938 20127355 + BAG6 chr6 31639028 31652705 - FKRP chr19 46746046 46776988 + SOX2 chr3 181711925 181714436 + KPNA4 chr3 160495007 160565571 - ATP6AP1 chrX 154428645 154436516 + THRA chr17 40058290 40093867 + PTK7 chr6 43076307 43161719 + FAM107B chr10 14518557 14774897 - TRMT2A chr22 20111875 20117392 - AC068946.2 chr2 219209772 219222738 - YIF1B chr19 38303558 38317273 - FLOT1 chr6 30727709 30742732 - HSPA1B chr6 31827738 31830254 + DVL3 chr3 184155377 184173614 + EME2 chr16 1772810 1781708 + OAZ1 chr19 2269509 2273490 + SLC37A4 chr11 119024114 119030906 - DDB1 chr11 61299451 61342596 - LAMB2 chr3 49121114 49133118 - SLC19A1 chr21 45493572 45573365 - NKRF chrX 119588337 119606443 - LOXL1 chr15 73925989 73952137 + TMBIM1 chr2 218274197 218292586 - APBB1 chr11 6395124 6419414 - ADNP2 chr18 80109262 80147523 + AFF4 chr5 132875395 132963634 - SENP3-EIF4A1 chr17 7563287 7578715 + SMG1 chr16 18804853 18926454 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC016876.2 chr17 7581964 7584086 - AD000090.1 chr19 35557956 35581954 + 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.