exRNAdisease

Entry Detail

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General Information

Database ID: exR0000356 RNA Name: AGA RNA Type: mRNA Chromosome: chr4 Starnd: - Coordinate: Start Site(bp): 177430774 End Site(bp): 177442437 External Links: ENSG00000038002

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 ANAPC4 chr4 25377213 25418498 + ATP6V1H chr8 53715543 53843558 - BTF3 chr5 73498408 73505635 + CAPN1 chr11 65180566 65212006 + CAT chr11 34438934 34472060 + CCDC169 chr13 36222008 36297840 - CCDC169-SOHLH2 chr13 36168794 36297842 - CHD8 chr14 21385194 21456126 - FADS2 chr11 61792980 61867354 + FAM107B chr10 14518557 14774897 - MCM2 chr3 127598410 127622436 + MRPL3 chr3 131462212 131502983 - MTRNR2L12 chr3 96617188 96618236 - PFN1 chr17 4945652 4949061 - PPM1A chr14 60245752 60299087 + PTGES3 chr12 56663341 56688408 - PUM3 chr9 2720469 2844095 - RPL13A chr19 49487554 49492308 + RPL27A chr11 8682788 8714759 + RPL5 chr1 92832013 92841924 + RPL8 chr8 144789765 144792587 - RPS20 chr8 56067295 56074581 - SPNS1 chr16 28974221 28984548 + SRGN chr10 69088103 69104805 + TAF7 chr5 141260225 141320784 - TMBIM6 chr12 49707725 49764934 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC109460.3 chr16 28974804 28990775 + LOH12CR2 chr12 12355406 12357067 - 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.