|
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
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|
|
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 |