exRNAdisease

Entry Detail

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General Information

Database ID: exR0000368 RNA Name: AGBL5 RNA Type: mRNA Chromosome: chr2 Starnd: + Coordinate: Start Site(bp): 27042364 End Site(bp): 27070622 External Links: ENSG00000084693

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 CD151 chr11 832887 839831 + WDR70 chr5 37379285 37753435 + PCNA chr20 5114953 5126626 - MRPL20 chr1 1401909 1407293 - EIF4B chr12 53006158 53042209 + CBS chr21 43053191 43076943 - SMC4 chr3 160399274 160434954 + SCD chr10 100347233 100364826 + AMMECR1L chr2 127861630 127885922 - LIFR chr5 38474668 38608354 - XPO6 chr16 28097979 28211920 - HNRNPA1 chr12 54280193 54287088 + IGFBP2 chr2 216632828 216664436 + TALDO1 chr11 747415 765012 + SYVN1 chr11 65121780 65134533 - RAB8A chr19 16111889 16134234 + FNBP1 chr9 129887187 130043194 - POLR2E chr19 1086574 1095380 - SNX25 chr4 185204237 185370185 + FAM76B chr11 95768953 95790409 - RPL4 chr15 66498015 66524532 - CREBZF chr11 85659708 85682908 - SNU13 chr22 41673933 41690504 - PSMB5 chr14 23016543 23035230 - TOX4 chr14 21476597 21499175 + RPL10 chrX 154389955 154409168 + ENTPD4 chr8 23385783 23457695 - URGCP-MRPS24 chr7 43866558 43906589 - MRPS24 chr7 43866558 43869893 - TIMM50 chr19 39480412 39493785 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC002470.2 chr22 20979462 20998121 + AC026362.1 chr12 122975320 122982907 + AL139819.1 chr10 100335563 100346390 - 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.