SRX23801529 GSM8121405_r1 SRP492696 PRJNA1082390 SRS20624511 GSM8121405 GSM8121405 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Tumor tissue was collected and chopped into small pieces. Digestion medium was added (RPMI containing 1mg/mL collagenase IV (Worthington Biochemical Corporation), 40 μg/mL DNase I (Roche 04716728001) and 2% heat-inactivated FCS) and incubated for 30 minutes at 37 °C. Cells were rinsed through a 70 μm cell strainer to obtain single-cell suspensions. To remove debris, Lympholyte®-M (CEDARLANE) was used according to manufacturer's instructions. Enriched tumor infiltrating leukocytes were stained and sorted (CD45+ DRAQ7-) using a Biorad S3 sorter in PBS with 1% BSA. Cellular suspension was loaded on a 10× Genomics Chromium instrument. Single-cell RNA-Seq libraries were prepared using Chromium Single Cell 3′ v3.1 Reagent Kit with dual indexes according to manufacturer's protocol. Library quantification and quality assessment was performed using a Qubit fluorometer (ThermoFisher Scientific) and a Tapestation (DNA High sensitivity chip - Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq 6000 using paired-end 28 × 90 bp as sequencing mode. Illumina NovaSeq 6000 SRX23801530 GSM8121406_r1 SRP492696 PRJNA1082390 SRS20624512 GSM8121406 GSM8121406 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Tumor tissue was collected and chopped into small pieces. Digestion medium was added (RPMI containing 1mg/mL collagenase IV (Worthington Biochemical Corporation), 40 μg/mL DNase I (Roche 04716728001) and 2% heat-inactivated FCS) and incubated for 30 minutes at 37 °C. Cells were rinsed through a 70 μm cell strainer to obtain single-cell suspensions. To remove debris, Lympholyte®-M (CEDARLANE) was used according to manufacturer's instructions. Enriched tumor infiltrating leukocytes were stained and sorted (CD45+ DRAQ7-) using a Biorad S3 sorter in PBS with 1% BSA. Cellular suspension was loaded on a 10× Genomics Chromium instrument. Single-cell RNA-Seq libraries were prepared using Chromium Single Cell 3′ v3.1 Reagent Kit with dual indexes according to manufacturer's protocol. Library quantification and quality assessment was performed using a Qubit fluorometer (ThermoFisher Scientific) and a Tapestation (DNA High sensitivity chip - Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq 6000 using paired-end 28 × 90 bp as sequencing mode. Illumina NovaSeq 6000 SRX23801531 GSM8121407_r1 SRP492696 PRJNA1082390 SRS20624513 GSM8121407 GSM8121407 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Tumor tissue was collected and chopped into small pieces. Digestion medium was added (RPMI containing 1mg/mL collagenase IV (Worthington Biochemical Corporation), 40 μg/mL DNase I (Roche 04716728001) and 2% heat-inactivated FCS) and incubated for 30 minutes at 37 °C. Cells were rinsed through a 70 μm cell strainer to obtain single-cell suspensions. To remove debris, Lympholyte®-M (CEDARLANE) was used according to manufacturer's instructions. Enriched tumor infiltrating leukocytes were stained and sorted (CD45+ DRAQ7-) using a Biorad S3 sorter in PBS with 1% BSA. Cellular suspension was loaded on a 10× Genomics Chromium instrument. Single-cell RNA-Seq libraries were prepared using Chromium Single Cell 3′ v3.1 Reagent Kit with dual indexes according to manufacturer's protocol. Library quantification and quality assessment was performed using a Qubit fluorometer (ThermoFisher Scientific) and a Tapestation (DNA High sensitivity chip - Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq 6000 using paired-end 28 × 90 bp as sequencing mode. Illumina NovaSeq 6000 SRX23801532 GSM8121408_r1 SRP492696 PRJNA1082390 SRS20624514 GSM8121408 GSM8121408 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Tumor tissue was collected and chopped into small pieces. Digestion medium was added (RPMI containing 1mg/mL collagenase IV (Worthington Biochemical Corporation), 40 μg/mL DNase I (Roche 04716728001) and 2% heat-inactivated FCS) and incubated for 30 minutes at 37 °C. Cells were rinsed through a 70 μm cell strainer to obtain single-cell suspensions. To remove debris, Lympholyte®-M (CEDARLANE) was used according to manufacturer's instructions. Enriched tumor infiltrating leukocytes were stained and sorted (CD45+ DRAQ7-) using a Biorad S3 sorter in PBS with 1% BSA. Cellular suspension was loaded on a 10× Genomics Chromium instrument. Single-cell RNA-Seq libraries were prepared using Chromium Single Cell 3′ v3.1 Reagent Kit with dual indexes according to manufacturer's protocol. Library quantification and quality assessment was performed using a Qubit fluorometer (ThermoFisher Scientific) and a Tapestation (DNA High sensitivity chip - Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq 6000 using paired-end 28 × 90 bp as sequencing mode. Illumina NovaSeq 6000 SRX23801533 GSM8121409_r1 SRP492696 PRJNA1082390 SRS20624515 GSM8121409 GSM8121409 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Tumor tissue was collected and chopped into small pieces. Digestion medium was added (RPMI containing 1mg/mL collagenase IV (Worthington Biochemical Corporation), 40 μg/mL DNase I (Roche 04716728001) and 2% heat-inactivated FCS) and incubated for 30 minutes at 37 °C. Cells were rinsed through a 70 μm cell strainer to obtain single-cell suspensions. To remove debris, Lympholyte®-M (CEDARLANE) was used according to manufacturer's instructions. Enriched tumor infiltrating leukocytes were stained and sorted (CD45+ DRAQ7-) using a Biorad S3 sorter in PBS with 1% BSA. Cellular suspension was loaded on a 10× Genomics Chromium instrument. Single-cell RNA-Seq libraries were prepared using Chromium Single Cell 3′ v3.1 Reagent Kit with dual indexes according to manufacturer's protocol. Library quantification and quality assessment was performed using a Qubit fluorometer (ThermoFisher Scientific) and a Tapestation (DNA High sensitivity chip - Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq 6000 using paired-end 28 × 90 bp as sequencing mode. Illumina NovaSeq 6000 SRX23801534 GSM8121410_r1 SRP492696 PRJNA1082390 SRS20624516 GSM8121410 GSM8121410 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Tumor tissue was collected and chopped into small pieces. Digestion medium was added (RPMI containing 1mg/mL collagenase IV (Worthington Biochemical Corporation), 40 μg/mL DNase I (Roche 04716728001) and 2% heat-inactivated FCS) and incubated for 30 minutes at 37 °C. Cells were rinsed through a 70 μm cell strainer to obtain single-cell suspensions. To remove debris, Lympholyte®-M (CEDARLANE) was used according to manufacturer's instructions. Enriched tumor infiltrating leukocytes were stained and sorted (CD45+ DRAQ7-) using a Biorad S3 sorter in PBS with 1% BSA. Cellular suspension was loaded on a 10× Genomics Chromium instrument. Single-cell RNA-Seq libraries were prepared using Chromium Single Cell 3′ v3.1 Reagent Kit with dual indexes according to manufacturer's protocol. Library quantification and quality assessment was performed using a Qubit fluorometer (ThermoFisher Scientific) and a Tapestation (DNA High sensitivity chip - Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq 6000 using paired-end 28 × 90 bp as sequencing mode. Illumina NovaSeq 6000 SRX23801535 GSM8121411_r1 SRP492696 PRJNA1082390 SRS20624518 GSM8121411 GSM8121411 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Tumor tissue was collected and chopped into small pieces. Digestion medium was added (RPMI containing 1mg/mL collagenase IV (Worthington Biochemical Corporation), 40 μg/mL DNase I (Roche 04716728001) and 2% heat-inactivated FCS) and incubated for 30 minutes at 37 °C. Cells were rinsed through a 70 μm cell strainer to obtain single-cell suspensions. To remove debris, Lympholyte®-M (CEDARLANE) was used according to manufacturer's instructions. Enriched tumor infiltrating leukocytes were stained and sorted (CD45+ DRAQ7-) using a Biorad S3 sorter in PBS with 1% BSA. Cellular suspension was loaded on a 10× Genomics Chromium instrument. Single-cell RNA-Seq libraries were prepared using Chromium Single Cell 3′ v3.1 Reagent Kit with dual indexes according to manufacturer's protocol. Library quantification and quality assessment was performed using a Qubit fluorometer (ThermoFisher Scientific) and a Tapestation (DNA High sensitivity chip - Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq 6000 using paired-end 28 × 90 bp as sequencing mode. Illumina NovaSeq 6000 SRX23801536 GSM8121412_r1 SRP492696 PRJNA1082390 SRS20624517 GSM8121412 GSM8121412 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA Tumor tissue was collected and chopped into small pieces. Digestion medium was added (RPMI containing 1mg/mL collagenase IV (Worthington Biochemical Corporation), 40 μg/mL DNase I (Roche 04716728001) and 2% heat-inactivated FCS) and incubated for 30 minutes at 37 °C. Cells were rinsed through a 70 μm cell strainer to obtain single-cell suspensions. To remove debris, Lympholyte®-M (CEDARLANE) was used according to manufacturer's instructions. Enriched tumor infiltrating leukocytes were stained and sorted (CD45+ DRAQ7-) using a Biorad S3 sorter in PBS with 1% BSA. Cellular suspension was loaded on a 10× Genomics Chromium instrument. Single-cell RNA-Seq libraries were prepared using Chromium Single Cell 3′ v3.1 Reagent Kit with dual indexes according to manufacturer's protocol. Library quantification and quality assessment was performed using a Qubit fluorometer (ThermoFisher Scientific) and a Tapestation (DNA High sensitivity chip - Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq 6000 using paired-end 28 × 90 bp as sequencing mode. Illumina NovaSeq 6000