Intratumoral CD8+ T cells with a tissue-resident phenotype mediate local immunity and immune checkpoint responses in breast cancer

Raw scRNA-seq fastq files: SS_V_1_HGYKJDRXX_CATGAACA_L001_R1.fastq.gz SS_V_1_HGYKJDRXX_CATGAACA_L001_R2.fastq.gz SS_V_1_HGYKJDRXX_CATGAACA_L002_R1.fastq.gz SS_V_1_HGYKJDRXX_CATGAACA_L002_R2.fastq.gz SS_V_2_HGYKJDRXX_TCACTCGC_L001_R1.fastq.gz SS_V_2_HGYKJDRXX_TCACTCGC_L001_R2.fastq.gz SS_V_2_HGYKJDRXX_TCACTCGC_L002_R1.fastq.gz SS_V_2_HGYKJDRXX_TCACTCGC_L002_R2.fastq.gz SS_V_3_HGYKJDRXX_AGCTGGAT_L001_R1.fastq.gz SS_V_3_HGYKJDRXX_AGCTGGAT_L001_R2.fastq.gz SS_V_3_HGYKJDRXX_AGCTGGAT_L002_R1.fastq.gz SS_V_3_HGYKJDRXX_AGCTGGAT_L002_R2.fastq.gz SS_V_4_HGYKJDRXX_GTGACTTG_L001_R1.fastq.gz SS_V_4_HGYKJDRXX_GTGACTTG_L001_R2.fastq.gz SS_V_4_HGYKJDRXX_GTGACTTG_L002_R1.fastq.gz SS_V_4_HGYKJDRXX_GTGACTTG_L002_R2.fastq.gz Raw single cell VDJ sequencing files: SS_VDJ_V_1_HGYKJDRXX_GCGAGAGT_L001_R1.fastq.gz SS_VDJ_V_1_HGYKJDRXX_GCGAGAGT_L001_R2.fastq.gz SS_VDJ_V_1_HGYKJDRXX_GCGAGAGT_L002_R1.fastq.gz SS_VDJ_V_1_HGYKJDRXX_GCGAGAGT_L002_R2.fastq.gz SS_VDJ_V_2_HGYKJDRXX_TACGTTCA_L001_R1.fastq.gz SS_VDJ_V_2_HGYKJDRXX_TACGTTCA_L001_R2.fastq.gz SS_VDJ_V_2_HGYKJDRXX_TACGTTCA_L002_R1.fastq.gz SS_VDJ_V_2_HGYKJDRXX_TACGTTCA_L002_R2.fastq.gz SS_VDJ_V_3_HGYKJDRXX_AGTCCCAC_L001_R1.fastq.gz SS_VDJ_V_3_HGYKJDRXX_AGTCCCAC_L001_R2.fastq.gz SS_VDJ_V_3_HGYKJDRXX_AGTCCCAC_L002_R1.fastq.gz SS_VDJ_V_3_HGYKJDRXX_AGTCCCAC_L002_R2.fastq.gz SS_VDJ_V_4_HGYKJDRXX_CTATAGTG_L001_R1.fastq.gz SS_VDJ_V_4_HGYKJDRXX_CTATAGTG_L001_R2.fastq.gz SS_VDJ_V_4_HGYKJDRXX_CTATAGTG_L002_R1.fastq.gz SS_VDJ_V_4_HGYKJDRXX_CTATAGTG_L002_R2.fastq.gz Raw single cell hashing sequencing: SS-V_S4_R1_001.fastq.gz SS-V_S4_R2_001.fastq.gz Processed Seurat object: tils.obj.rdata Process VDJ sequencing data: all_contig_annotations.csv