exRNAdisease

Entry Detail

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General Information

Database ID: exR0000373 RNA Name: AGK RNA Type: mRNA Chromosome: chr7 Starnd: + Coordinate: Start Site(bp): 141551278 End Site(bp): 141655244 External Links: ENSG00000006530

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 EXOSC6 chr16 70246778 70251940 - AL138752.2 chr9 37588413 38068687 - TUBA1C chr12 49188736 49274603 + TOMM5 chr9 37582646 37592604 - RTN3 chr11 63681446 63759891 + LSS chr21 46188141 46228824 - SESN3 chr11 95165513 95232541 - RPAP2 chr1 92299059 92402056 + CBX5 chr12 54230942 54280133 - TAF10 chr11 6606294 6612539 - ID2 chr2 8678845 8684461 + ZCCHC17 chr1 31296982 31364953 + RBM5 chr3 50088919 50119021 + ZNF426 chr19 9523223 9538645 - ITGAL chr16 30472719 30523185 + KDM1A chr1 23019443 23083689 + ITGB5 chr3 124761948 124901418 - ARIH2 chr3 48918821 48986382 + PUF60 chr8 143816344 143829352 - GALC chr14 87837820 87993665 - AL513165.2 chr9 37512547 37592469 - PSMA2 chr7 42916861 42932185 - LGR4 chr11 27365961 27472790 - C5orf38 chr5 2752131 2755397 + ABI1 chr10 26746593 26861087 - AC010132.3 chr7 42909273 42932174 - LSM4 chr19 18306230 18323274 - FBXO21 chr12 117141988 117190531 - MRPL15 chr8 54135241 54148514 + HNRNPL chr19 38836388 38852347 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC097634.1 chr3 71584943 71587409 + GUSBP11 chr22 23638487 23717356 - PURPL chr5 27217714 27496994 + SNHG1 chr11 62851984 62855953 - XIST chrX 73820649 73852723 - 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.