exRNAdisease

Entry Detail

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General Information

Database ID: exR0000231 RNA Name: ADAM17 RNA Type: mRNA Chromosome: chr2 Starnd: - Coordinate: Start Site(bp): 9488486 End Site(bp): 9556732 External Links: ENSG00000151694

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 ITM2C chr2 230864639 230879248 + HUNK chr21 31873020 32044633 + TPGS2 chr18 36777647 36829216 - MOCS3 chr20 50958818 50963929 + ESCO2 chr8 27771949 27812640 + COMMD1 chr2 61888724 62147247 + TMX1 chr14 51240162 51257655 + NACA chr12 56712427 56731628 - ELOVL5 chr6 53267398 53349179 - KHDRBS1 chr1 32013868 32060850 + PSMA2 chr7 42916861 42932185 - PTMA chr2 231706895 231713541 + GATAD1 chr7 92447482 92460075 + SLC30A9 chr4 41990502 42090461 + SUGP2 chr19 18990888 19034023 - CCT5 chr5 10249929 10266389 + RNF44 chr5 176526712 176538025 - ATP5MC3 chr2 175176258 175184607 - G6PC3 chr17 44070735 44076344 + ZSCAN30 chr18 35251058 35290245 - MDN1 chr6 89642498 89819794 - GSTP1 chr11 67583742 67586656 + MARCKSL1 chr1 32333839 32336233 - PSMD2 chr3 184299198 184309050 + XPO6 chr16 28097979 28211920 - EIF3A chr10 119033670 119080823 - AL136454.1 chr1 192716132 192716653 + PIK3CA chr3 179148114 179240093 + COL11A2 chr6 33162681 33192499 - ZNF24 chr18 35332227 35345482 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand BX284668.2 chr1 16870945 16883659 + LINC01783 chr1 16533886 16536172 - 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.