exRNAdisease

Entry Detail

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General Information

Database ID: exR0000122 RNA Name: ACAP2 RNA Type: mRNA Chromosome: chr3 Starnd: - Coordinate: Start Site(bp): 195274745 End Site(bp): 195443044 External Links: ENSG00000114331

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 SERPINB5 chr18 63476958 63505085 + RPS23 chr5 82273320 82278396 - MTRNR2L12 chr3 96617188 96618236 - KRT8 chr12 52897187 52949954 - TMEM63A chr1 225845536 225882380 - CDCA7L chr7 21900899 21945903 - SSBP4 chr19 18418864 18434562 + RAB34 chr17 28714281 28718429 - ATG4C chr1 62784132 62865516 + MT-ND3 chrMT 10059 10404 + CYFIP2 chr5 157266079 157395595 + DCTN6 chr8 30156319 30183639 + ACAP3 chr1 1292390 1309609 - CREB1 chr2 207529737 207605988 + CLU chr8 27596917 27614700 - COQ4 chr9 128322544 128334072 + ZFR chr5 32354350 32444740 - FLVCR1 chr1 212858275 212899363 + HLA-DRA chr6 32439878 32445046 + ACOT1 chr14 73537143 73543796 + ANAPC15 chr11 72106378 72112780 - SBNO1 chr12 123289109 123364847 - AAK1 chr2 69457997 69674349 - C20orf204 chr20 64034344 64039962 + HSD17B11 chr4 87336515 87391188 - PRKCA chr17 66302613 66810743 + MT-CO3 chrMT 9207 9990 + LCP1 chr13 46125920 46211871 - NRDC chr1 51789191 51878937 - ERP29 chr12 112013348 112023449 + miRNA targets: miRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand hsa-miR-320a-3p chr8 22244975 22244996 - hsa-miR-320b chr1 224257049 224257070 - hsa-miR-320c chr18 24321716 24321735 + hsa-miR-320d chr13 40727828 40727846 - circRNA targets: NA lncRNA targets: NA 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.