exRNAdisease

Entry Detail

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General Information

Database ID: exR0008321 RNA Name: MARCKS RNA Type: mRNA Chromosome: chr6 Starnd: + Coordinate: Start Site(bp): 113857345 End Site(bp): 113863475 External Links: ENSG00000277443

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 ABT1 chr6 26596953 26600739 + AC009133.6 chr16 29812261 29820092 + AC010422.3 chr19 12643831 12648397 - AC011448.1 chr19 19516227 19536076 + AC048338.1 chr12 122207779 122266423 - AC087289.3 chr17 75898645 75930129 - ACKR3 chr2 236567787 236582354 + ACOT7 chr1 6264269 6394391 - ADAM15 chr1 155050566 155062775 + ADAR chr1 154582057 154628013 - ADCY1 chr7 45574140 45723116 + ADD3 chr10 109996368 110135565 + ADGRA3 chr4 22345071 22516066 - ADGRL2 chr1 81306160 81992436 + ADPRHL1 chr13 113399610 113453524 - AGPAT5 chr8 6708642 6761503 + ALDH9A1 chr1 165662216 165698863 - miRNA targets: miRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand hsa-miR-19a-3p chr13 91350939 91350961 + hsa-miR-146a-5p chr5 160485372 160485393 + circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC010478.1 chr5 51372736 51383332 - AC016394.2 chr10 73252791 73254349 + AC090114.2 chr7 128524016 128531069 - AC112907.3 chr3 186781780 186784179 - 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.