exRNAdisease

Entry Detail

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General Information

Database ID: exR0000420 RNA Name: AIMP2 RNA Type: mRNA Chromosome: chr7 Starnd: + Coordinate: Start Site(bp): 6009255 End Site(bp): 6023834 External Links: ENSG00000106305

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 AC026954.2 chr17 7312661 7319174 - RPL36 chr19 5674947 5691875 + TFG chr3 100709331 100748964 + CCDC163 chr1 45493866 45500079 - RPL19 chr17 39200283 39204732 + PAICS chr4 56435741 56464579 + CDK16 chrX 47217860 47229997 + AC139530.2 chr17 81703371 81720539 + IMP3 chr15 75639085 75648706 - EPN1 chr19 55675226 55709858 + NDUFV1 chr11 67605653 67612554 + BFAR chr16 14632931 14669236 + PRR13 chr12 53441678 53446645 + NMT1 chr17 45051610 45109016 + EEF2 chr19 3976056 3985463 - FTSJ3 chr17 63819433 63830012 - CYP51A1 chr7 92112153 92134803 - BZW1 chr2 200810594 200827338 + MIF chr22 23894383 23895227 + MCL1 chr1 150574551 150579738 - DYNLL1 chr12 120469850 120498493 + SNX30 chr9 112750760 112881671 + SMO chr7 129188633 129213545 + GLUL chr1 182381704 182392206 - KDM4B chr19 4969113 5153598 + FBRS chr16 30658431 30670810 + RNASEK-C17orf49 chr17 7012635 7017520 + NFE2L1 chr17 48048329 48061545 + CTSB chr8 11842524 11869448 - CTNNBL1 chr20 37693955 37872129 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC245014.3 chr1 145281116 145281462 + AD000090.1 chr19 35557956 35581954 + ATP2B1-AS1 chr12 89708959 89712590 + STAG3L5P-PVRIG2P-PILRB chr7 100336104 100367831 + TPT1-AS1 chr13 45341345 45417975 + 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.