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Sample GSM5470533 Query DataSets for GSM5470533
Status Public on Jul 26, 2021
Title OC10.1
Sample type SRA
 
Source name Oseochondroma
Organism Homo sapiens
Characteristics subject: Patient #10
disease state: Oseochondroma
tissue: Osteochondroma explant
treated drug: Vehicle ethanol
concentration: 0.1%v/v
Treatment protocol Osteochondroma explants were treated with NRX202467 or Palovarotene at 50-300nM.
Growth protocol Cartilage caps were microdissected from human osteochondromas obtained at surgery, miced into 3-5 mm cubic and cultured inside a diffusion chamber
Extracted molecule total RNA
Extraction protocol Osteochondroma explants were washed with PBS, stored in RNAlator and kept at -80C. The explants were placed on clean Kimwipe to absorb excess RNAlater solution and then were snap-frozen in liquid nitrogen. Frozen tissue fragments were placed on pre-chilled carbon steel block and crashed into powder by the steel hammer. We then purified total RNA using Qiagen RNeasy fibrous tissue mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing Raw data were analyzed using the Hisat aligner with stand-specific settings.
Differential gene expression was analyzed using the DESeq R package (Bioconductor) and the negative binomial model
Criteria for significant differences in gene expression were (1) false discovery rate (FDR) <0.05, (2) expression level >10th percentile, and (3) ≥ 2-fold change. 
Genome_build: Homo sapiens GRCh38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample
 
Submission date Jul 24, 2021
Last update date Jul 27, 2021
Contact name Carrie McCracken
E-mail(s) cmccracken@som.umaryland.edu
Organization name Institute of Genome
Department Institute for Genome Sciences
Street address 670 W. Baltimore St
City Baltimore
State/province MD
ZIP/Postal code 21201
Country USA
 
Platform ID GPL20301
Series (2)
GSE180764 Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes of Osteochondroma Explants Nontreated or Treated with Selective Agonist of Retionic acid Nuclear Receptor Gamma (RARg) I
GSE181133 Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes of Osteochondroma Explants Nontreated or Treated with Selective Agonist of Retionic acid Nuclear Receptor Gamma (RARg)
Relations
BioSample SAMN20370384
SRA SRX11542354

Supplementary file Size Download File type/resource
GSM5470533_OC10_1.accepted_hits.sorted_by_position.genic.coverage.stats.rpkm.txt.gz 1.3 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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