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Sample GSM7833084 Query DataSets for GSM7833084
Status Public on Feb 06, 2024
Title Pat16
Sample type SRA
Source name melanoma
Organism Homo sapiens
Characteristics tissue: melanoma
treatment: anti-CTLA4 resistant
gender: F
Stage: M1c
type.of.primary: skin
previous. brafi: yes_Before
prior.ctla4i: TRUE
groups: anti-CTLA4 resistant
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
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
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.
Submission date Oct 10, 2023
Last update date Feb 06, 2024
Contact name Martin Lauss
Organization name Lund University
Department Dept of Oncology
Street address Barngatan 2B
City Lund
ZIP/Postal code 22185
Country Sweden
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

Supplementary data files not provided
Raw data not provided for this record

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