exRNAdisease

Entry Detail

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General Information

Database ID: exR0000053 RNA Name: ABCC5 RNA Type: mRNA Chromosome: chr3 Starnd: - Coordinate: Start Site(bp): 183919934 End Site(bp): 184017939 External Links: ENSG00000114770

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 VAPA chr18 9914002 9960021 + DGKQ chr4 958887 986895 - STRADA chr17 63682336 63741986 - POFUT1 chr20 32207880 32238658 + DSTN chr20 17570075 17609919 + EEF1D chr8 143579697 143599541 - STRA6 chr15 74179466 74212267 - WDR43 chr2 28894667 28948219 + TMEM63A chr1 225845536 225882380 - OBSL1 chr2 219550728 219571859 - RITA1 chr12 113185526 113192368 + MKRN1 chr7 140453033 140479536 - BSG chr19 571277 583493 + CALM3 chr19 46601074 46610782 + RPL37 chr5 40825262 40835222 - PLEKHG3 chr14 64704102 64750249 + SMAD4 chr18 51028394 51085045 + SNX5 chr20 17941597 17968980 - PPP2R3B chrX 333933 386955 - SCMH1 chr1 41027200 41242154 - LCK chr1 32251239 32286165 + SIK2 chr11 111602449 111730855 + PPP2R1B chr11 111726908 111766389 - SNX2 chr5 122775079 122834543 + KLHL23 chr2 169694488 169776989 + RAB4B-EGLN2 chr19 40778242 40808418 + WDR86 chr7 151375909 151410727 - REPS1 chr6 138903493 138988261 - PABPC3 chr13 25095868 25099254 + PROCA1 chr17 28703197 28711854 - miRNA targets: miRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand hsa-miR-185-5p chr22 20033153 20033174 + hsa-miR-423-5p chr17 30117095 30117117 + hsa-miR-1323 chr19 53671978 53671999 + hsa-miR-548o-3p chr20 38516607 38516628 + circRNA targets: NA lncRNA targets: NA 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.