exRNAdisease

Entry Detail

---



General Information

Database ID: exR0000080 RNA Name: ABHD16A RNA Type: mRNA Chromosome: chr6 Starnd: - Coordinate: Start Site(bp): 31686955 End Site(bp): 31703356 External Links: ENSG00000204427

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 CBSL chr21 6444869 6468040 - FBXO45 chr3 196568611 196589059 + SENP6 chr6 75601509 75718281 + ZNF711 chrX 85244032 85273362 + WLS chr1 68098473 68233120 - RPA1 chr17 1829702 1900082 + ARID1B chr6 156776020 157210779 + GCN1 chr12 120127202 120194715 - FASTKD5 chr20 3146519 3159865 - VIPR1 chr3 42489299 42537573 + MRPL54 chr19 3762682 3768575 + RPL18 chr19 48615328 48619184 - CHD1 chr5 98853985 98928957 - TRAF4 chr17 28744005 28750956 + PTMS chr12 6765516 6770952 + FLNC chr7 128830377 128859274 + RAB1B chr11 66268590 66277492 + UCHL1 chr4 41256413 41268455 + CBS chr21 43053191 43076943 - NOL6 chr9 33461353 33473930 - TMEM50A chr1 25338317 25362361 + SLC39A1 chr1 153959099 153968184 - MAF chr16 79585843 79600737 - PACSIN2 chr22 42835412 43015149 - MOB2 chr11 1469457 1501247 - GJA1 chr6 121435595 121449727 + LIG3 chr17 34980512 35009743 + RPS27L chr15 63125872 63158021 - SLC25A28 chr10 99610522 99620609 - CCT7 chr2 73233420 73253021 + miRNA targets: NA circRNA targets: NA lncRNA targets: NA 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.