exRNAdisease

Entry Detail

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General Information

Database ID: exR0000376 RNA Name: AGO1 RNA Type: mRNA Chromosome: chr1 Starnd: + Coordinate: Start Site(bp): 35869808 End Site(bp): 35930532 External Links: ENSG00000092847

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 MT-ND4L chrMT 10470 10766 + ESPL1 chr12 53268299 53293638 + SAMD4B chr19 39342396 39385710 + CANX chr5 179678628 179731641 + NFATC2IP chr16 28950807 28967097 + LAMTOR1 chr11 72085895 72103297 - PSMD2 chr3 184299198 184309050 + AP1B1 chr22 29327680 29423179 - PJA2 chr5 109334713 109409974 - KDM4B chr19 4969113 5153598 + REC8 chr14 24171853 24180257 + PTMA chr2 231706895 231713541 + HLA-A chr6 29941260 29945884 + FTO chr16 53701692 54158512 + KRIT1 chr7 92198969 92246166 - DNMBP chr10 99875577 100009947 - AP002990.1 chr11 62559603 62591531 - RPL36AL chr14 49618530 49620626 - SMS chrX 21940709 21994837 + SPINT2 chr19 38244035 38292615 + KLHL36 chr16 84648511 84667686 + PANX1 chr11 94128841 94181968 + CALM1 chr14 90396502 90408268 + PRPF40A chr2 152651593 152717997 - AGO2 chr8 140520156 140635633 - NEURL4 chr17 7315628 7329393 - RPL32 chr3 12834485 12841582 - RPL8 chr8 144789765 144792587 - LCOR chr10 96832282 96995959 + SND1 chr7 127652194 128092609 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC023509.1 chr12 53441741 53467528 + AC007347.1 chr16 54033997 54054583 - AC022034.3 chr8 53394110 53484067 - LINC01641 chr1 227393554 227431035 + TUG1 chr22 30969245 30979395 + 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.