exRNAdisease

Entry Detail

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General Information

Database ID: exR0000162 RNA Name: ACP6 RNA Type: mRNA Chromosome: chr1 Starnd: - Coordinate: Start Site(bp): 147629652 End Site(bp): 147670524 External Links: ENSG00000162836

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 ABHD12 chr20 25294742 25390835 - ACSL1 chr4 184755595 184826818 - BICD2 chr9 92711363 92764833 - CHERP chr19 16517894 16542437 - CHRNB1 chr17 7445061 7457710 + COX4I1 chr16 85798633 85807068 + CPSF1 chr8 144393229 144409335 - DERL3 chr22 23834503 23839128 - DST chr6 56457987 56954649 - FBXO4 chr5 41925254 41941743 + GDE1 chr16 19501693 19522123 - GLCE chr15 69160584 69272217 + GLIS3 chr9 3824127 4348392 - IFITM1 chr11 313506 315272 + IFITM2 chr11 307631 315272 + NUP214 chr9 131125586 131234663 + PARP14 chr3 122680839 122730840 + PCNA chr20 5114953 5126626 - PHF21B chr22 44881162 45010005 - PKM chr15 72199029 72231822 - PPRC1 chr10 102132994 102150333 + RPL11 chr1 23691742 23696835 + RPL5 chr1 92832013 92841924 + SCD chr10 100347233 100364826 + TGFBRAP1 chr2 105264391 105329735 - TRAM2 chr6 52497408 52577060 - TUBG2 chr17 42659284 42667006 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC113189.4 chr17 7439506 7445966 + 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.