exRNAdisease

Entry Detail

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General Information

Database ID: exR0000123 RNA Name: ACAP3 RNA Type: mRNA Chromosome: chr1 Starnd: - Coordinate: Start Site(bp): 1292390 End Site(bp): 1309609 External Links: ENSG00000131584

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 IMP3 chr15 75639085 75648706 - TAOK2 chr16 29973868 29992261 + SDCBP chr8 58552924 58582859 + NUP62 chr19 49906825 49929763 - ALG1 chr16 5033923 5087379 + EEF2 chr19 3976056 3985463 - S100A13 chr1 153618787 153631360 - RUNX3 chr1 24899511 24965121 - SLC15A4 chr12 128793194 128823958 - HAND1 chr5 154474972 154478227 - MTOR chr1 11106535 11262551 - SENP3 chr17 7561919 7571969 + MIF chr22 23894383 23895227 + SLC7A5 chr16 87830023 87869507 - MT-ND4 chrMT 10760 12137 + DEPDC5 chr22 31753867 31908033 + SLC27A2 chr15 50182196 50236385 + XPO6 chr16 28097979 28211920 - PCSK1N chrX 48831096 48835610 - KMT2B chr19 35717973 35738878 + MCM3AP chr21 46235133 46286297 - PFKM chr12 48105139 48146404 + TUBA4A chr2 219249710 219278170 - CLTC chr17 59619689 59696956 + PIK3C2B chr1 204422628 204494724 - TRIM7 chr5 181193924 181205293 - HIRA chr22 19330698 19447450 - AURKAIP1 chr1 1373730 1375495 - SETD1A chr16 30957754 30984664 + ZFHX4 chr8 76681239 76867281 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AL157392.3 chr10 13631143 13668445 + AL355075.4 chr14 20343048 20343685 - XIST chrX 73820649 73852723 - 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.