exRNAdisease

Entry Detail

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General Information

Database ID: exR0000030 RNA Name: ABCA3 RNA Type: mRNA Chromosome: chr16 Starnd: - Coordinate: Start Site(bp): 2275881 End Site(bp): 2340746 External Links: ENSG00000167972

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 ATG2B chr14 96279195 96363341 - BCAR1 chr16 75228181 75268053 - LAMB2 chr3 49121114 49133118 - HLA-F chr6 29722775 29738528 + NOC4L chr12 132144457 132152473 + HS3ST3A1 chr17 13494032 13601929 - ASRGL1 chr11 62337448 62393412 + HNRNPUL2-BSCL2 chr11 62690275 62727384 - SIK3 chr11 116843402 117098437 - MCMBP chr10 119829404 119892556 - CYB5R3 chr22 42617840 42649392 - RPL11 chr1 23691742 23696835 + KLHL21 chr1 6590724 6614607 - PVRIG chr7 100218241 100221490 + ZNF219 chr14 21090077 21104722 - PKM chr15 72199029 72231822 - HMGB2 chr4 173331376 173334432 - DNAJC18 chr5 139408588 139444491 - MT-ND4L chrMT 10470 10766 + CHTF18 chr16 788046 800737 + CDH4 chr20 61252261 61940617 + TSC2 chr16 2047967 2089491 + CDCA2 chr8 25459199 25507911 + TPRN chr9 137191617 137204193 - HLA-E chr6 30489509 30494194 + DCP2 chr5 112976702 113022195 + FAM104A chr17 73207353 73236753 - BUB3 chr10 123154402 123170467 + RFWD3 chr16 74621399 74666877 - TUBB2A chr6 3153666 3157544 - miRNA targets: NA circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC022167.2 chr16 8848105 8860456 + AC245014.3 chr1 145281116 145281462 + XIST chrX 73820649 73852723 - 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.