exRNAdisease

Entry Detail

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General Information

Database ID: exR0015571 RNA Name: TUBA1B RNA Type: mRNA Chromosome: chr12 Starnd: - Coordinate: Start Site(bp): 49127782 End Site(bp): 49131397 External Links: ENSG00000123416

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 ADIPOR1 chr1 202940826 202958572 - AKIRIN1 chr1 38991276 39006059 + AEN chr15 88621337 88632281 + ADCY5 chr3 123282296 123449758 - ALDOA chr16 30064164 30070457 + AK2 chr1 33007940 33080996 - ADRM1 chr20 62302093 62308862 + ABRACL chr6 139028745 139043302 + ACSS2 chr20 34872146 34927962 + AGFG2 chr7 100539203 100568220 + ACTN4 chr19 38647649 38731589 + AGBL5 chr2 27042364 27070622 + ABI2 chr2 203328239 203447728 + AC008878.3 chr19 7382834 7470241 + ADGRG6 chr6 142301854 142446266 + ACVR2B chr3 38453890 38493142 + AC120057.2 chr17 7240427 7244635 - AC138811.2 chr16 18788063 18801519 - ABHD14A-ACY1 chr3 51974706 51989183 + ADD1 chr4 2843857 2930076 + AC004922.1 chr7 99325879 99394653 + ADSL chr22 40346500 40390463 + ACTG1 chr17 81509971 81523847 - ADA chr20 44619522 44652233 - AC007192.1 chr19 18153158 18178117 + AC007040.2 chr2 70939318 70995336 - AC015813.2 chr17 57989038 58007246 - ADAR chr1 154582057 154628013 - AC011448.1 chr19 19516227 19536076 + AL136454.1 chr1 192716132 192716653 + miRNA targets: miRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand hsa-miR-103a-3p chr5 168560904 168560926 - hsa-miR-106a-5p chrX 134170244 134170266 - hsa-miR-221-3p chrX 45746180 45746202 - hsa-miR-302c-3p chr4 112648366 112648388 - hsa-miR-652-3p chrX 110055389 110055409 + hsa-miR-1291 chr12 48654494 48654517 - hsa-miR-3654 chr7 133034860 133034878 - hsa-miR-4707-5p chr14 22956998 22957020 - circRNA targets: NA lncRNA targets: lncRNA Symbol Chromosome Start Site(bp) End Site(bp) Strand AC005618.1 chr5 141326210 141329357 + AC007952.4 chr17 19112000 19112636 - AC012485.1 chr2 238231684 238255633 + AC016876.2 chr17 7581964 7584086 - AC022167.2 chr16 8848105 8860456 + AC023509.1 chr12 53441741 53467528 + AC026362.1 chr12 122975320 122982907 + AC069281.2 chr7 100572232 100578700 - AC087190.3 chr16 9104848 9113181 + AC104461.1 chr1 200333193 200478669 + AC124067.3 chr8 37559992 37567477 + AC245014.3 chr1 145281116 145281462 + AD000090.1 chr19 35557956 35581954 + AL049543.1 chr6 28587378 28591747 + AL118516.1 chr22 46761894 46762563 - 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.