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68 results for “TCR-seq”

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zenodo36/100

Single-cell RNA-Seq and TCR-Seq analysis of PD-1+ CD8+ T-cells responding to anti-PD-1 and anti-PD-1/CTLA-4 immunotherapy in melanoma

This dataset details the scRNASeq and TCR-Seq analysis of sorted PD-1+ CD8+ T cells from patients with melanoma treated with checkpoint therapy (anti-PD-1 monotherapy and anti-PD-1 & anti-CTLA-4 combination therapy) at baseline and after the first cycle of therapy. A major publication using this dataset is accessible here: (reference)     *experimental design  Single-cell RNA sequencing was performed using 10x Genomics with feature barcoding technology to multiplex cell samples from different patients undergoing mono or dual therapy so that they can be loaded on one well to reduce costs and minimize technical variability. Hashtag oligomers (oligos) were obtained as purified and already oligo-conjugated in TotalSeq-C format from BioLegend. Cells were thawed, counted and 20 million cells per patient and time point were used for staining. Cells were stained with barcoded antibodies together with a staining solution containing antibodies against CD3, CD4, CD8, PD-1/IgG4 and fixable viability dye (eBioscience) prior to FACS sorting. Barcoded antibody concentrations used were 0.5 µg per million cells, as recommended by the manufacturer (BioLegend) for flow cytometry applications. After staining, cells were washed twice in PBS containing 2% BSA and 0.01% Tween 20, followed by centrifugation (300 xg 5 min at 4 °C) and supernatant exchange. After the final wash, cells were resuspended in PBS and filtered through 40 µm cell strainers and proceeded for sorting. Sorted cells were counted and approximately 75,000 cells were processed through 10x Genomics single-cell V(D)J workflow according to the manufacturer’s instructions. Gene expression, hashing and TCR libraries were pooled to desired quantities to obtain the sequencing depths of 15,000 reads per cell for gene expression libraries and 5,000 reads per cell for hashing and TCR libraries. Libraries were sequenced on a NovaSeq 6000 flow cell in a 2X100 paired-end format.   *extract protocol  PBMCs were thawed, counted and 20 million cells per patient and time point were used for staining. Cells were stained with barcoded antibodies together with a staining solution containing antibodies against CD3, CD4, CD8, PD-1/IgG4 and fixable viability dye (eBioscience) prior to FACS sorting. Barcoded antibody concentrations used were 0.5 µg per million cells, as recommended by the manufacturer (BioLegend) for flow cytometry applications. After staining, cells were washed twice in PBS containing 2% BSA and 0.01% Tween 20, followed by centrifugation (300 xg 5 min at 4 °C) and supernatant exchange. After the final wash, cells were resuspended in PBS and filtered through 40 µm cell strainers and proceeded for sorting. Sorted cells were counted and approximately 75,000 cells were processed through 10x Genomics single-cell V(D)J workflow according to the manufacturer’s instructions.   *library construction protocol  Sorted cells were counted and approximately 75,000 cells were processed through 10x Genomics single-cell V(D)J workflow according to the manufacturer’s instructions. Gene expression, hashing and TCR libraries were pooled to desired quantities to obtain the sequencing depths of 15,000 reads per cell for gene expression libraries and 5,000 reads per cell for hashing and TCR libraries. Libraries were sequenced on a NovaSeq 6000 flow cell in a 2X100 paired-end format.   *library strategy  scRNA-seq and scTCR-seq   *data processing step  Pre-processing of sequencing results to generate count matrices (gene expression and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline.  Further processing was done with Seurat (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis based on gene expression).    *genome build/assembly  Alignment was performed using prebuilt Cell Ranger human reference GRCh38.   *processed data files format and content  RNA counts and HTO counts are in sparse matrix format and TCR clonotypes are in csv format. Datasets were merged and analyzed by Seurat and the analyzed objects are in rds format.   <table> <tbody> <tr> <td> file name </td> <td> file checksum </td> </tr> <tr> <td> PD1CD8_160421_filtered_feature_bc_matrix.zip </td> <td> da2e006d2b39485fd8cf8701742c6d77 </td> </tr> <tr> <td> PD1CD8_190421_filtered_feature_bc_matrix.zip </td> <td> e125fc5031899bba71e1171888d78205 </td> </tr> <tr> <td> PD1CD8_160421_filtered_contig_annotations.csv </td> <td> 927241805d507204fbe9ef7045d0ccf4 </td> </tr> <tr> <td> PD1CD8_190421_filtered_contig_annotations.csv </td> <td> 8ca544d27f06e66592b567d3ab86551e </td> </tr> </tbody> </table>    <table> <tbody> <tr> <td> *processed data file </td> <td> antibodies/tags </td> </tr> <tr> <td> PD1CD8_160421_filtered_feature_bc_matrix.zip </td> <td> none </td> </tr> <tr> <td> PD1CD8_160421_filtered_feature_bc_matrix.zip </td> <td> TotalSeq™-C0251 anti-human Hashtag 1 Antibody - (HASH_1) - M1_base_monotherapy TotalSeq™-C0252 anti-human Hashtag 2 Antibody - (HASH_2) - M1_post_monotherapy TotalSeq™-C0253 anti-human Hashtag 3 Antibody - (HASH_3) - C1_base_combined_therapy TotalSeq™-C0254 anti-human Hashtag 4 Antibody - (HASH_4) - C1_post_combined_therapy TotalSeq™-C0255 anti-human Hashtag 5 Antibody - (HASH_5) - C2_base_combined_therapy TotalSeq™-C0256 anti-human Hashtag 6 Antibody - (HASH_6) - C2_post_combined_therapy </td> </tr> <tr> <td> PD1CD8_160421_filtered_contig_annotations.csv </td> <td> none </td> </tr> <tr> <td> PD1CD8_190421_filtered_feature_bc_matrix.zip </td> <td> none </td> </tr> <tr> <td> PD1CD8_190421_filtered_feature_bc_matrix.zip </td> <td> TotalSeq™-C0251 anti-human Hashtag 1 Antibody - (HASH_1) - M2_base_monotherapy TotalSeq™-C0252 anti-human Hashtag 2 Antibody - (HASH_2) - M2_post_monotherapy TotalSeq™-C0253 anti-human Hashtag 3 Antibody - (HASH_3) - M3_base_monotherapy TotalSeq™-C0254 anti-human Hashtag 4 Antibody - (HASH_4) - M3_post_monotherapy TotalSeq™-C0255 anti-human Hashtag 5 Antibody - (HASH_5) - C3_base_combined_therapy TotalSeq™-C0256 anti-human Hashtag 6 Antibody - (HASH_6) - C3_post_combined_therapy </td> </tr> <tr> <td> PD1CD8_190421_filtered_contig_annotations.csv </td> <td> none </td> </tr> </tbody> </table>

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Dataset results

Single-cell RNA-Seq and TCR-Seq analysis of PD-1+ CD8+ T-cells responding to anti-PD-1 and anti-PD-1/CTLA-4 immunotherapy in melanoma

RELB Reprograms Exhausted Tumor-Infiltrating Lymphocytes for Improved Adoptive Cell Therapy [TCR-Seq]

Neoadjuvant PARPi or Chemotherapy in Ovarian Cancer Informs Targeting Effector Treg Cells for Homologous-Recombination-Deficient Tumors [bulk TCR-seq]

TCR-seq of each iNKT subset isolated from the thymus of BALB/c and B6 mice

Assessing the impact of TET2 and TET3 deletion in TCRa and TCRb expression and repertoire in murine CD4 T cells in physiological and pathological conditions [TCR-seq]

Chimeric antigen receptor macrophages (CAR-M) sensitize HER2+ solid tumors to PD1 blockade [TCR-Seq]

Durable Suppression of Acquired MEK Inhibitor Resistance in Cancer by Sequestering MEK from ERK and Promoting Anti-Tumor T-cell Immunity [TCR-seq]

Profiling of Sarcomas from Archival Tissues [TCR-Seq]

Analysis of local mucosal immune dysregulation to guide pilot directed therapy for long-COVID olfactory loss [TCR-seq]

Reverse translational discovery reveals dysregulation of CD4+ and CD8+ resident memory T, myeloid, and stromal cells in steroid-refractory, checkpoint inhibitor colitis [biopsy scRNA_TCR-seq]

BCL6-dependent TCF-1+ progenitor cells maintain effector and helper CD4 T cell responses to persistent antigen [TCR-seq]

Polyclonal lymphoid expansion drives paraneoplastic autoimmunity in neuroblastoma [TCR-Seq]

Melanoma Brain Metastasis Atlas [TCR-Seq]

Single-cell transcriptomic analysis of tissue resident memory T cells in human lung cancer [TCR-seq]

scRNA and TCR-Seq of peripheral blood mononuclear cells (PBMC) from r/r classical Hodgkin Lymphoma patients under anti-PD1 therapy.

Integrated Single-Cell and Spatial Transcriptomics Uncover Distinct Cellular Subtypes Involved in Neural Invasion in PDAC [TCR-Seq]

Complementary HLH Susceptibility Factors Converge on CD8 T-cell Hyperactivation [TCR-seq]

Distinct transcriptional programs characterize neoantigen-specific T cells in lung cancers treated with neoadjuvant PD-1 blockade [bulk TCR-seq]

Measuring anti-islet autoimmunity in mouse and human by profiling peripheral blood antigen specific CD4 T cells [TCR-Seq]

CD8+ T-cell memory induced by successive SARS-CoV-2 mRNA vaccinations is characterized by clonal replenishment [AIM Bulk TCR-seq]

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