exRNAdisease

Entry Detail

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General Information

Database ID: exR0011541 RNA Name: PTMS RNA Type: mRNA Chromosome: chr12 Starnd: + Coordinate: Start Site(bp): 6765516 End Site(bp): 6770952 External Links: ENSG00000159335

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 AARSD1 chr17 42950526 42964498 - ABCG2 chr4 88090150 88231628 - ABHD16A chr6 31686955 31703356 - ABHD8 chr19 17292131 17310236 - ABI1 chr10 26746593 26861087 - AC010422.3 chr19 12643831 12648397 - AC011462.1 chr19 41350853 41425001 + AC073508.2 chr17 40627356 40665141 - AC073896.1 chr12 56285916 56316059 - AC087289.3 chr17 75898645 75930129 - AC131160.1 chr3 183815568 183884889 - AC245033.1 chr15 82536788 82573194 - ACIN1 chr14 23058564 23095614 - ACO2 chr22 41469117 41528989 + ACTB chr7 5527148 5563784 - ACTG1 chr17 81509971 81523847 - ACTN1 chr14 68874143 68979440 - ACTR3 chr2 113890063 113962596 + AHCY chr20 34280268 34311802 - AKAP13 chr15 85380571 85749358 + AL136454.1 chr1 192716132 192716653 + AL162417.1 chr9 133098121 133163914 - ALDH16A1 chr19 49453225 49471050 + 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-708-5p chr11 79402077 79402099 - hsa-miR-1294 chr5 154347153 154347174 + hsa-miR-1270 chr19 20399320 20399342 - hsa-miR-1276 chr15 85770548 85770567 - hsa-miR-3917 chr1 25906384 25906403 - circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC006064.5 chr12 6510275 6510522 + AC006460.2 chr2 190607660 190649840 - AC125807.2 chr12 3041437 3044950 + AC245033.4 chr15 82533175 82540008 - AL117378.1 chr6 131901963 131920565 + 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.