exRNAdisease

Entry Detail

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General Information

Database ID: exR0000414 RNA Name: AIFM1 RNA Type: mRNA Chromosome: chrX Starnd: - Coordinate: Start Site(bp): 130129362 End Site(bp): 130165887 External Links: ENSG00000156709

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 FKBP8 chr19 18531751 18544077 - RPL13A chr19 49487554 49492308 + DAPK3 chr19 3958453 3971123 - RPS19 chr19 41860255 41872925 + RPS21 chr20 62387103 62388520 + TARS2 chr1 150487364 150507609 + CHKA chr11 68052859 68121444 - NUP50 chr22 45163925 45188017 + FADS2 chr11 61792980 61867354 + RPS28 chr19 8321158 8323340 + RPLP1 chr15 69452814 69456205 + MXI1 chr10 110207605 110287365 + RPL36 chr19 5674947 5691875 + BCAP31 chrX 153700492 153724565 - AKAP11 chr13 42272152 42323261 + EPS8L2 chr11 694438 727727 + ACTR3 chr2 113890063 113962596 + WDCP chr2 24029347 24049575 - HEATR1 chr1 236549005 236604516 - DEGS1 chr1 224175756 224193441 + CCNG1 chr5 163437569 163446151 + RBM14 chr11 66616582 66627347 + GPBP1 chr5 57173948 57264679 + PTPN7 chr1 202147013 202161588 - AC058822.1 chr4 53377839 54295272 + EVL chr14 99971449 100144236 + ZNF451 chr6 57086844 57170305 + HCLS1 chr3 121631399 121660927 - EGLN3 chr14 33924227 34462774 - OAZ1 chr19 2269509 2273490 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC064802.1 chr8 114282067 114295839 + AC013269.1 chr2 130530275 130537182 + ITGB2-AS1 chr21 44921051 44929678 + JPX chrX 73944182 74070408 + SNHG14 chr15 24978583 25420336 + 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.