exRNAdisease

Entry Detail

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General Information

Database ID: exR0000381 RNA Name: AGPAT2 RNA Type: mRNA Chromosome: chr9 Starnd: - Coordinate: Start Site(bp): 136673143 End Site(bp): 136687457 External Links: ENSG00000169692

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 ABCA7 chr19 1039997 1065572 + ARF1 chr1 228082660 228099212 + CSNK1E chr22 38290691 38318084 - DNAJB6 chr7 157335381 157417439 + ENO1 chr1 8861000 8879190 - EP300 chr22 41092592 41180077 + EZR chr6 158765741 158819368 - FTL chr19 48965309 48966879 + GEMIN5 chr5 154887411 154938211 - ILF3 chr19 10654261 10692417 + ITM2C chr2 230864639 230879248 + MTA1 chr14 105419820 105470729 + MYD88 chr3 38138478 38143022 + NELFE chr6 31952087 31959038 - NKX3-2 chr4 13540830 13544508 - PLXNA3 chrX 154458281 154477779 + POLD1 chr19 50384204 50418018 + QPRT chr16 29663279 29698699 + RPL13A chr19 49487554 49492308 + RPS15 chr19 1438358 1440494 + SRSF4 chr1 29147743 29181900 - TNK2 chr3 195863364 195911945 - TRAPPC12 chr2 3379675 3485094 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC019205.1 chr6 73263212 73301789 + 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.