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| Status |
Public on Feb 06, 2024 |
| Title |
Pat17 |
| Sample type |
SRA |
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| Source name |
melanoma
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| Organism |
Homo sapiens |
| Characteristics |
tissue: melanoma
treatment: anti-CTLA4 resistant
gender: M
Stage: M1c
type.of.primary: mucosa
previous. brafi: no_
prior.ctla4i: TRUE
groups: mucosal
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tumor DNA and RNA was extracted using AllPrep DNA/RNA Mini Kit (Qiagen)
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 NextSeq 500 |
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| Data processing |
RNA sequencing data of bulk tumor samples were aligned using HISAT2 version 2.1.0 and reference hg38.analysisSet_gencode27_snp150, and further processed using StringTie to obtain FPKM values.
Transcripts with the same gene name were added up. The data were reduced to protein-coding genes.
The data were transformed as log2(data+1) and quantile-normalized using limma. Six samples that did not undergo ICB treatment were removed.
Principal Component (PC) PC2 was associated with a batch variable and was removed from the data using R package swamp.
Assembly: hg38
Supplementary files format and content: tab-delimited text file that includes FPKM values, which have undergone log-transformation, quantile-normalization and removal of PC2.
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| Submission date |
Oct 10, 2023 |
| Last update date |
Feb 06, 2024 |
| Contact name |
Martin Lauss |
| Organization name |
Lund University
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| Department |
Dept of Oncology
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| Street address |
Barngatan 2B
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| City |
Lund |
| ZIP/Postal code |
22185 |
| Country |
Sweden |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE244982 |
Molecular patterns of resistance to immune checkpoint blockade in melanoma [bulk RNA-Seq] |
| GSE244984 |
Molecular patterns of resistance to immune checkpoint blockade in melanoma |
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| Supplementary data files not provided |
| Raw data not provided for this record |
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