exRNAdisease

Entry Detail

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General Information

Database ID: exR0000447 RNA Name: AKAP8 RNA Type: mRNA Chromosome: chr19 Starnd: - Coordinate: Start Site(bp): 15353385 End Site(bp): 15379798 External Links: ENSG00000105127

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 ANAPC7 chr12 110372900 110403730 - SHQ1 chr3 72749277 72861914 - ZNF500 chr16 4748239 4767624 - UBN1 chr16 4846665 4882401 + CALR chr19 12938578 12944489 + ICE2 chr15 60419609 60479160 - L1TD1 chr1 62194849 62212328 + TRIP12 chr2 229763838 229923239 - ZNF43 chr19 21804949 21852125 - GMPS chr3 155870650 155944020 + ABCC1 chr16 15949577 16143074 + RPL36A-HNRNPH2 chrX 101391011 101412297 + BAMBI chr10 28677510 28682932 + NACA2 chr17 61590421 61591219 - ZZEF1 chr17 4004445 4143030 - PPP1R12C chr19 55090914 55117637 - TLE3 chr15 70047790 70098176 - NCL chr2 231453531 231483641 - DCAF10 chr9 37800554 37867666 + MIXL1 chr1 226223618 226227054 + NAT10 chr11 34105617 34147670 + ALDOA chr16 30064164 30070457 + MON1B chr16 77190835 77202398 + TIMMDC1 chr3 119498547 119525090 + SH3PXD2A chr10 103594027 103855543 - ATF6B chr6 32115264 32128253 - CDK7 chr5 69234795 69277430 + RIPOR1 chr16 67518418 67546788 + NPC2 chr14 74476192 74494177 - CACNG6 chr19 53992288 54012669 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AL355075.4 chr14 20343048 20343685 - LINC01248 chr2 5602505 5691488 - 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.