exRNAdisease

Entry Detail

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General Information

Database ID: exR0000189 RNA Name: ACTG2 RNA Type: mRNA Chromosome: chr2 Starnd: + Coordinate: Start Site(bp): 73892314 End Site(bp): 73919865 External Links: ENSG00000163017

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 POTEE chr2 131218067 131265278 + ACTG1 chr17 81509971 81523847 - GADD45A chr1 67685201 67688334 + LSM11 chr5 157743712 157760709 + NGRN chr15 90265659 90278141 + MTRNR2L1 chr17 22523111 22524663 + CNN1 chr19 11538767 11550323 + BOLA1 chr1 149887890 149900798 + NBEAL1 chr2 203014879 203226378 + HNRNPA2B1 chr7 26173057 26201529 - LRPPRC chr2 43886224 43995989 - SNX17 chr2 27370496 27377535 + PPIG chr2 169584344 169641406 + SLC25A3 chr12 98593591 98606379 + SYPL1 chr7 106090503 106112576 - MCM3AP chr21 46235133 46286297 - POTEI chr2 130459455 130509707 - ACTA2 chr10 88935074 88991339 - COMT chr22 19941733 19969975 + RAB10 chr2 26034084 26137454 + ANP32A chr15 68778535 68820897 - ASB3 chr2 53532672 53860160 - PKM chr15 72199029 72231822 - CAMP chr3 48223347 48225491 + POTEJ chr2 130611481 130658091 + SDHA chr5 218241 257082 + HSP90B1 chr12 103930107 103953645 + WNT5B chr12 1529891 1647212 + ACTB chr7 5527148 5563784 - ACTC1 chr15 34790230 34795549 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC013269.1 chr2 130530275 130537182 + AL359924.1 chr1 237862175 237928321 + EIF1B-AS1 chr3 40061110 40309698 - 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.