exRNAdisease

Entry Detail

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General Information

Database ID: exR0000313 RNA Name: ADK RNA Type: mRNA Chromosome: chr10 Starnd: + Coordinate: Start Site(bp): 74151202 End Site(bp): 74709963 External Links: ENSG00000156110

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 CLTC chr17 59619689 59696956 + CORO1C chr12 108645109 108731596 - BCL2L1 chr20 31664452 31723989 - C12orf57 chr12 6942978 6946003 + IFI6 chr1 27666064 27672198 - RAB11FIP3 chr16 425649 523011 + GDI2 chr10 5765223 5842132 - GRWD1 chr19 48445841 48457022 + BCKDHA chr19 41397808 41425002 + DGKZ chr11 46332905 46380554 + IGF2 chr11 2129112 2141238 - PRMT1 chr19 49675786 49689029 + GJA1 chr6 121435595 121449727 + KRT19 chr17 41523617 41528308 - HLA-DPA1 chr6 33064569 33080775 - EIF3E chr8 108201216 108435333 - INO80B-WBP1 chr2 74455088 74460884 + TRIO chr5 14143342 14532128 + MTRNR2L8 chr11 10507894 10509186 - PTPN1 chr20 50510321 50585241 + ZNF664 chr12 123971845 124015439 + MRPL35 chr2 86199355 86213790 + CCNG1 chr5 163437569 163446151 + STAU1 chr20 49113339 49188367 - NBEAL1 chr2 203014879 203226378 + HMGN3 chr6 79201245 79234738 - RPS27L chr15 63125872 63158021 - ENO1 chr1 8861000 8879190 - UBE2J2 chr1 1253909 1273885 - TMED7 chr5 115613210 115632992 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC007952.4 chr17 19112000 19112636 - AC132217.1 chr11 2129121 2129964 - AD000090.1 chr19 35557956 35581954 + IGF2-AS chr11 2140501 2148666 + 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.