exRNAdisease

Entry Detail

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General Information

Database ID: exR0000417 RNA Name: AIG1 RNA Type: mRNA Chromosome: chr6 Starnd: + Coordinate: Start Site(bp): 143060496 End Site(bp): 143341058 External Links: ENSG00000146416

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 NARS2 chr11 78435968 78574874 - MYO1G chr7 44962662 44979088 - ARHGAP30 chr1 161046946 161069970 - AREL1 chr14 74653437 74713108 - UBE3A chr15 25333728 25439051 - ATP2B4 chr1 203626561 203744081 + DTWD1 chr15 49621037 49656232 + RND2 chr17 43025231 43032041 + CYP26A1 chr10 93073475 93077885 + RGS12 chr4 3293028 3439913 + MT-CO2 chrMT 7586 8269 + ATRX chrX 77504878 77786233 - AC131160.1 chr3 183815568 183884889 - HSP90AB1 chr6 44246166 44253888 + DPP8 chr15 65442463 65517704 - PPP1R8 chr1 27830782 27851676 + EIF4B chr12 53006158 53042209 + FKBP1A chr20 1368978 1393172 - TUBB chr6 30720352 30725426 + HS1BP3 chr2 20560448 20651130 - ARRB2 chr17 4710596 4721499 + RNH1 chr11 494512 507300 - BOD1 chr5 173607145 173616659 - RPLP1 chr15 69452814 69456205 + GNAS chr20 58839718 58911192 + WDR12 chr2 202874782 203014798 - SLC43A3 chr11 57406954 57427580 - ST3GAL2 chr16 70375977 70439237 - TEX10 chr9 100302077 100352942 - IGFBP4 chr17 40443450 40457725 + miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC137630.2 chr3 48979918 48983985 - HOTAIRM1 chr7 27095647 27100265 + 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.