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Sample GSM5487810 Query DataSets for GSM5487810
Status Public on Jul 30, 2021
Title OC5.7
Sample type SRA
 
Source name Oseochondroma
Organism Homo sapiens
Characteristics patient: Patient #5
treated drug: NRX204647
concentration: 300 nM
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 2000
 
Data processing Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software
The STAR aligner uses a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Using DESeq2, a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate p-values and Log2 fold changes.
Genome_build: The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Supplementary_files_format_and_content: tab-delimted text files include counts values for each sample
 
Submission date Jul 29, 2021
Last update date Jul 31, 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 GPL11154
Series (2)
GSE181129 Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes of Osteochondroma Explants Nontreated or Treated with Selective Agonist of Retionic acid Nuclear Receptor Gamma (RARg) II
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 SAMN20491648
SRA SRX11603733

Supplementary file Size Download File type/resource
GSM5487810_OC5-7.counts.txt.gz 4.3 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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