exRNAdisease

Entry Detail

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General Information

Database ID: exR0000307 RNA Name: ADI1 RNA Type: mRNA Chromosome: chr2 Starnd: - Coordinate: Start Site(bp): 3497366 End Site(bp): 3519531 External Links: ENSG00000182551

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 ENO3 chr17 4948092 4957131 + GNL2 chr1 37566816 37595937 - ZNF485 chr10 43606419 43617904 + CYTH2 chr19 48469208 48482314 + APP chr21 25880550 26171128 - RPL36 chr19 5674947 5691875 + SLC44A2 chr19 10602457 10644557 + PAICS chr4 56435741 56464579 + TMSB4X chrX 12975110 12977227 + RPS14 chr5 150442635 150449739 - SERPING1 chr11 57597387 57614848 + STC2 chr5 173314713 173329503 - LIMS1 chr2 108534355 108687246 + SMARCA4 chr19 10960825 11079426 + TTLL6 chr17 48762235 48817214 - MORF4L2 chrX 103675496 103688158 - ADD3 chr10 109996368 110135565 + SLC11A2 chr12 50979401 51028566 - RWDD3 chr1 95234210 95247225 + HNRNPAB chr5 178204533 178211163 + QPRT chr16 29663279 29698699 + TCF7L1 chr2 85133392 85310387 + CIZ1 chr9 128161251 128204383 - SFSWAP chr12 131711081 131799737 + MFN1 chr3 179347709 179394936 + OCIAD1 chr4 48805212 48861817 + CCT7 chr2 73233420 73253021 + VANGL2 chr1 160400564 160428670 + U2AF1L5 chr21 6484623 6499261 - SNX3 chr6 108211222 108261246 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC009446.1 chr8 71675300 71702786 + AC022400.6 chr10 73703735 73713581 - 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.