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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 28, 2022 |
| Title |
B16_PD1_TLR_65 |
| Sample type |
SRA |
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| Source name |
Tumor_tissue
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| Organism |
Mus musculus |
| Characteristics |
tissue: Tumor tissue
treatment: aPD1 antibody + TLR agonist mix
strain: C57BL/6J
tumor model: subcutanous injection of B16F10 melanoma
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from fresh frozen (FF) tissue with the RNeasy Mini Kit (Qiagen) and from FFPE tissue with the RSC RNA FFPE Kit (Maxwell, San Diego, CA). Both where used according to manufacturer’s instructions.
Only FF or FFPE samples were compared among each other. 3´mRNA libraries were generated from total RNA using the Lexogen QuantSeq kit according to the standard protocol. After validation (2200 TapeStation, Agilent Technologies, Santa Clara, CA) and quantification (Qubit System, Invitrogen, Carlsbad, California) pools of cDNA libraries were generated. The pools were quantified using the KAPA Library Quantification kit (Peqlab, Radnor, PA) and the 7900HT Sequence Detection System (Applied Biosystems, Foster City, PA) and subsequently sequenced on an Illumina HiSeq4000 or NovaSeq6000 sequencer .
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Fig-3.txt
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| Data processing |
FASTQ files of 3’ UTR RNA-sequencing were checked for quality using FastQC (version 0.11.4).
Reads were mapped to the mouse reference genome GRCm38 (p6) using the STAR aligner (version 2.7.0).
Expression was quantified prior to downstream analysis with RSEM (version 1.3.1).
Analyses were run on the computing cluster of the Regional Computing Center of the University of Cologne (RRZK).
Gene expression of specific genes was compared by comparing z-scores of counts per million (CPM).
Genome_build: mm10
Supplementary_files_format_and_content: tab separated .txt files are provided. One processed data file is provided for each one of three experiments which each consist of multiple experimental groups. Within each experiment data has been z-score normalized. Each column contains processed data from one sample and can be identified with the same identifier as each sample's raw data
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| Submission date |
Apr 22, 2021 |
| Last update date |
Oct 28, 2022 |
| Contact name |
Sven Borchmann |
| E-mail(s) |
sven.borchmann@uk-koeln.de
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| Organization name |
University Of Cologne
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| Street address |
Weyertal 115c
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| City |
Cologne |
| ZIP/Postal code |
50937 |
| Country |
Germany |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE173107 |
Tripartite target-agnostic combination immunotherapy cures established poorly immunogenic tumors |
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| Relations |
| BioSample |
SAMN18834998 |
| SRA |
SRX10658752 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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