exRNAdisease

Entry Detail

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General Information

Database ID: exR0008426 RNA Name: MDK RNA Type: mRNA Chromosome: chr11 Starnd: + Coordinate: Start Site(bp): 46380756 End Site(bp): 46383837 External Links: ENSG00000110492

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 AC092143.1 chr16 89919165 89936092 + AEN chr15 88621337 88632281 + AKIRIN1 chr1 38991276 39006059 + AC013394.1 chr15 92883413 92949230 + ALDOA chr16 30064164 30070457 + AK2 chr1 33007940 33080996 - ADGRB1 chr8 142449430 142545009 + AHSA1 chr14 77457870 77469472 + ACTG1 chr17 81509971 81523847 - ABHD14A-ACY1 chr3 51974706 51989183 + AK4 chr1 65147549 65232145 + AC093525.2 chr16 2496032 2520218 + AL139011.2 chr1 160216800 160285130 - ADAT3 chr19 1905399 1913447 + AC008878.3 chr19 7382834 7470241 + AHNAK chr11 62433542 62556235 - ADIPOR1 chr1 202940826 202958572 - ABRACL chr6 139028745 139043302 + ABHD8 chr19 17292131 17310236 - AL121845.3 chr20 63708864 63739103 + AKR1A1 chr1 45550543 45570049 + AC058822.1 chr4 53377839 54295272 + ACY1 chr3 51983340 51989197 + AC093668.1 chr7 102541501 102592444 - ABL1 chr9 130713016 130887675 + AC007192.1 chr19 18153158 18178117 + AC011448.1 chr19 19516227 19536076 + AC245033.1 chr15 82536788 82573194 - ABCF1 chr6 30571393 30597179 + AC104581.2 chr17 7925931 7930622 - miRNA targets: miRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand hsa-miR-204-5p chr9 70810031 70810052 - hsa-miR-211-5p chr15 31065095 31065116 - hsa-miR-124-3p chr8 64379210 64379231 + hsa-miR-185-5p chr22 20033153 20033174 + hsa-miR-642a-5p chr19 45674943 45674964 + hsa-miR-624-3p chr14 31014669 31014689 - hsa-miR-3654 chr7 133034860 133034878 - circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC007952.4 chr17 19112000 19112636 - AC010615.2 chr19 21444241 21463908 - AC011468.2 chr19 52130548 52171533 - AC068134.2 chr2 232420661 232421461 - AC132217.1 chr11 2129121 2129964 - AD000090.1 chr19 35557956 35581954 + AL022311.1 chr22 37876148 37895563 + 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.