exRNAdisease

Entry Detail

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General Information

Database ID: exR0000342 RNA Name: AEBP2 RNA Type: mRNA Chromosome: chr12 Starnd: + Coordinate: Start Site(bp): 19404045 End Site(bp): 19720801 External Links: ENSG00000139154

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 DDX55 chr12 123602077 123620943 + NCKAP1 chr2 182909115 183038858 - AC092329.3 chr19 23222755 23274221 - FUS chr16 31180110 31194871 + HLA-F chr6 29722775 29738528 + EMD chrX 154379273 154381523 + MT-CO2 chrMT 7586 8269 + MSH5-SAPCD1 chr6 31740020 31764851 + BLOC1S2 chr10 100273280 100286680 - RAB11FIP4 chr17 31391675 31538211 + NYNRIN chr14 24399003 24419283 + ZNF724 chr19 23221599 23250390 - RPS28 chr19 8321158 8323340 + IRF2BPL chr14 77024543 77028708 - RACK1 chr5 181236897 181248096 - TTC9 chr14 70641916 70675366 + SAP18 chr13 21140514 21149084 + OCIAD1 chr4 48805212 48861817 + YBX1 chr1 42682418 42703805 + RHOBTB3 chr5 95713522 95824383 + NDUFB10 chr16 1959538 1961975 + HMGCR chr5 75336329 75362101 + NCS1 chr9 130172404 130237303 + TMEM43 chr3 14124940 14143679 + HNRNPA2B1 chr7 26173057 26201529 - COPB2 chr3 139355600 139389680 - NETO1 chr18 72742314 72868146 - RPL28 chr19 55385345 55403250 + RASGEF1C chr5 180100795 180209211 - DNAJB11 chr3 186567403 186585800 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AL139260.2 chr1 38839333 38874494 - AL139819.1 chr10 100335563 100346390 - AL357078.2 chr1 65003470 65004087 - LINC01694 chr21 45593654 45603088 + 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.