|
| Status |
Public on May 13, 2016 |
| Title |
IHRT907-Chondroblastoma-WT |
| Sample type |
SRA |
| |
|
| Source name |
patient tumor sample
|
| Organism |
Homo sapiens |
| Characteristics |
tumor type: chondroblastoma
genotype: histone H3 wildtype
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Flash-frozen tumor specimens were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw reads are trimmed for quality (phred33 >= 30) and length (n >= 30) using Trimmomatic (v. 0.32). Illumina adaptor sequences are clipped off using the palindromic mode.
Perform a sliding window trimming, cutting once the average quality within the window falls below 30. Cut 3 bases off the start of each read, if below quality 30. Cut 3 bases off the end of each read, if above quality 30. Cut the first 4 bases at the start of each read. Drop short reads (n <= 30).
Reads are aligned to the UCSC hg19 genome with STAR v2.3.0e using default settings, which removes multimapping reads. Feature annotation is provided by UCSC knownGene.
Read counting is done with featureCounts v1.4.4. Unless stated otherwise, default settings are used. Read summarization is done at the gene symbol level. The minimum mapping quality score for a read to be counted is 3. Only primary alignments are counted. Reads rather than fragments are counted. Only reads mapping to exons are considered.
Expression data is variance-stabilized using the VST algorithm provided by the DESeq2 R package.
Genome_build: hg19
Supplementary_files_format_and_content: tab separated file containing read counts normalized with the variance-stabilized transformation
|
| |
|
| Submission date |
Dec 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter W Lewis |
| E-mail(s) |
pwlewis2@wisc.edu
|
| Phone |
608-316-4388
|
| Organization name |
University of Wisconsin-Madison
|
| Department |
Department of Biomolecular Chemistry
|
| Lab |
Room 2174, Wisconsin Institute for Discovery
|
| Street address |
330 N Orchard Street
|
| City |
Madison |
| State/province |
Wisconsin |
| ZIP/Postal code |
53715 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE69291 |
H3K36 mutations promote sarcomagenesis through genome-wide remodeling of H3K36 and H3K27 methylation |
| GSE75853 |
H3K36 mutations promote sarcomagenesis through genome-wide remodeling of H3K36 and H3K27 methylation [RNA_Chondroblastoma_H3K36M_H3WT] |
|
| Relations |
| BioSample |
SAMN04328098 |
| SRA |
SRX1473005 |
