exRNAdisease

Entry Detail

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General Information

Database ID: exR0000391 RNA Name: AGTPBP1 RNA Type: mRNA Chromosome: chr9 Starnd: - Coordinate: Start Site(bp): 85546539 End Site(bp): 85742029 External Links: ENSG00000135049

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 COL5A1 chr9 134641803 134844843 + EEF2 chr19 3976056 3985463 - EPOP chr17 38671703 38674957 - CCDC88C chr14 91271323 91417844 - TADA2B chr4 7041899 7057952 + HNRNPK chr9 83968083 83980616 - RPS27A chr2 55231903 55235853 + PSMD3 chr17 39980807 39997959 + VAMP3 chr1 7771296 7781432 + GPRC5B chr16 19856691 19886167 - CCDC189 chr16 30757423 30762221 - CCAR2 chr8 22604632 22621514 + CAND2 chr3 12796472 12871916 + DNAJB6 chr7 157335381 157417439 + TPT1 chr13 45333471 45341370 - METTL7A chr12 50923472 50932510 + PLXNA3 chrX 154458281 154477779 + SMARCD1 chr12 50085200 50100707 + ST13 chr22 40824535 40856639 - U2SURP chr3 142964497 143060725 + ZNF234 chr19 44141554 44160313 + ABHD14B chr3 51968510 51983409 - TYMS chr18 657653 673578 + GATAD2B chr1 153789030 153923360 - STAT1 chr2 190908460 191020960 - RANBP1 chr22 20115938 20127355 + VTI1B chr14 67647085 67674820 - IRF4 chr6 391752 411443 + C1orf210 chr1 43281877 43285617 - CALM3 chr19 46601074 46610782 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand PDCD4-AS1 chr10 110869868 110872233 - ZFAS1 chr20 49278178 49299600 + 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.