|
| Status |
Public on Jul 30, 2021 |
| Title |
OC5.2 |
| Sample type |
SRA |
| |
|
| Source name |
Oseochondroma
|
| Organism |
Homo sapiens |
| Characteristics |
patient: Patient #5
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 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 |
SAMN20490672 |
| SRA |
SRX11603728 |
