exRNAdisease

Entry Detail

---



General Information

Database ID: exR0000066 RNA Name: ABCG2 RNA Type: mRNA Chromosome: chr4 Starnd: - Coordinate: Start Site(bp): 88090150 End Site(bp): 88231628 External Links: ENSG00000118777

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 PTMS chr12 6765516 6770952 + AP2B1 chr17 35578046 35726413 + PFN1 chr17 4945652 4949061 - ACKR3 chr2 236567787 236582354 + RFX5 chr1 151340640 151347357 - SUPT16H chr14 21351476 21384019 - ABHD14A-ACY1 chr3 51974706 51989183 + PLXNA2 chr1 208022242 208244384 - PDXDC1 chr16 14974591 15139339 + SDC2 chr8 96493813 96611790 + MORN3 chr12 121648742 121672631 - RARB chr3 25174332 25597932 + GNPDA1 chr5 141991749 142013041 - TPT1 chr13 45333471 45341370 - ZNRF2 chr7 30284597 30367689 + PSMA5 chr1 109399042 109426448 - ELF1 chr13 40931924 41061440 - PDHB chr3 58427630 58433857 - PSMA4 chr15 78540405 78552417 + CCND3 chr6 41934933 42050357 - NELFA chr4 1982717 2041903 - RPS3 chr11 75399515 75422280 + MTRNR2L12 chr3 96617188 96618236 - NMD3 chr3 161104696 161253532 + UGT3A2 chr5 36035021 36071358 - AFF4 chr5 132875395 132963634 - HNRNPA2B1 chr7 26173057 26201529 - CDH1 chr16 68737292 68835541 + SIPA1L1 chr14 71320449 71741229 + RPL9 chr4 39452521 39458949 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC078881.1 chr4 177442519 177681381 + AC069287.1 chr11 112967 125927 - NR2F1-AS1 chr5 93360779 93585649 - 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.