exRNAdisease

Entry Detail

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General Information

Database ID: exR0010595 RNA Name: PHC3 RNA Type: mRNA Chromosome: chr3 Starnd: - Coordinate: Start Site(bp): 170086732 End Site(bp): 170181749 External Links: ENSG00000173889

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 AAMP chr2 218264123 218270257 - ABR chr17 1003518 1229738 - ABTB2 chr11 34150987 34358010 - ACSS1 chr20 25006230 25058980 - ADD3 chr10 109996368 110135565 + miRNA targets: miRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand hsa-let-7a-5p chr9 94175962 94175983 + hsa-let-7b-5p chr22 46113691 46113712 + hsa-let-7d-5p chr9 94178841 94178862 + hsa-let-7e-5p chr19 51692793 51692814 + hsa-let-7f-5p chrX 53557246 53557267 - hsa-let-7g-5p chr3 52268336 52268357 - hsa-let-7i-5p chr12 62603691 62603712 + hsa-miR-150-5p chr19 49500832 49500853 - hsa-miR-373-3p chr19 53788748 53788770 + hsa-miR-432-5p chr14 100884496 100884518 + hsa-miR-520e-3p chr19 53675764 53675784 + hsa-miR-520a-3p chr19 53690933 53690954 + hsa-miR-520b-3p chr19 53701267 53701287 + hsa-miR-520c-3p chr19 53707506 53707527 + hsa-miR-520d-3p chr19 53720149 53720170 + hsa-miR-488-3p chr1 177029374 177029394 - hsa-miR-532-3p chrX 50003204 50003225 + hsa-miR-873-5p chr9 28888925 28888945 - 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.