exRNAdisease

Entry Detail

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General Information

Database ID: exR0000144 RNA Name: ACO1 RNA Type: mRNA Chromosome: chr9 Starnd: + Coordinate: Start Site(bp): 32384603 End Site(bp): 32454769 External Links: ENSG00000122729

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 UBA52 chr19 18571730 18577550 + SLC25A6 chrX 1386152 1392113 - PCGF3 chr4 705748 770640 + INSR chr19 7112255 7294414 - EEF2 chr19 3976056 3985463 - UNG chr12 109097574 109110992 + STRN4 chr19 46719511 46746994 - MIF chr22 23894383 23895227 + CRMP1 chr4 5748084 5893086 - TOP2A chr17 40388525 40417896 - RAB3D chr19 11322068 11346270 - RPL17 chr18 49488453 49492523 - RPL23 chr17 38847860 38853764 - TMEM250 chr9 136114581 136118875 - IGFBP5 chr2 216672105 216695549 - XRCC5 chr2 216107464 216206303 + RPL27 chr17 42998273 43002959 + ZNF681 chr19 23739195 23758891 - RLF chr1 40161387 40240921 + IMMT chr2 86143932 86195770 - ECD chr10 73130155 73169055 - PTPN11 chr12 112418351 112509913 + TPT1 chr13 45333471 45341370 - DAD1 chr14 22564907 22589224 - AKAP1 chr17 57085092 57121346 + CDCA7L chr7 21900899 21945903 - BID chr22 17734138 17774770 - WDR27 chr6 169457212 169702067 - CCT7 chr2 73233420 73253021 + CD274 chr9 5450503 5470566 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand OIP5-AS1 chr15 41283990 41309737 + 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.