Single cell T cell Landscape and T Cell Receptor Repertoire Profiling of AML in Context of PD-1 Blockade Therapy

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Dataset ID	Description	Technology	Samples
EGAD00001007671	Paired-end BAM files with associated index files of 15 AML samples were generated using Agilent SureSelect XT library capture system using a custom panel as described before Takahashi et al Blood 2018. Libraries were sequenced using Illumina HiSeq 2500.	Illumina HiSeq 2500	15
EGAD00001007672	Pared-end fastq files of 22 AML and 2 normal bone marrow samples were generated using 10x Genomics 5' single cell RNA sequencing following manufacturer's protocol (CG000086 User Guide RevG) for chemistry version 1.0 and targeting 10000 cells per sample. Libraries were sequenced using Illumina HiSeq 4000 using recommended cycling parameters.	Illumina HiSeq 4000	24
EGAD00001007673	Paired-end fastq files of 22 AML and 2 normal bone marrow samples were generated using 10x Genomics single cell BCR sequencing following manufacturer's protocol (CG000086 User Guide RevG) for chemistry version 1.0 and targeting 10000 cells per sample. Libraries were sequenced using Illumina NovaSeq 6000 using recommended cycling parameters.	Illumina NovaSeq 6000	24
EGAD00001007674	Paired-end fastq files of 22 AML and 2 normal bone marrow samples were generated using 10x Genomics single cell TCR sequencing following manufacturer's protocol (CG000086 User Guide RevG) for chemistry version 1.0 and targeting 10000 cells per sample. Libraries were sequenced using Illumina NovaSeq 6000 using recommended cycling parameters.	Illumina NovaSeq 6000	24
EGAD00001007675	Paired-end fastq files of 22 AML and 2 normal bone marrow samples were generated using 10x Genomics single cell ATAC sequencing following manufacturer's protocol (CG000168 User Guide RevB) for chemistry version 1.0 and targeting 10000 nuclei per sample. Libraries were sequenced using Illumina HiSeq4000 using recommended cycling parameters.	Illumina HiSeq 4000	24

Publications	Citations
Single cell T cell landscape and T cell receptor repertoire profiling of AML in context of PD-1 blockade therapy. Abbas HA, Hao D, Tomczak K, Barrodia P, Im JS, Reville PK, Alaniz Z, Wang W, Wang R, Wang F, Al-Atrash G, Takahashi K, Ning J, Ding M, Beird HC, Mathews JT, Little L, Zhang J, Basu S, Konopleva M, Marques-Piubelli ML, Solis LM, Parra ER, Lu W, Tamegnon A, Garcia-Manero G, Green MR, Sharma P, Allison JP, Kornblau SM, Rai K, Wang L, Daver N, Futreal A. Nat Commun 12: 2021 6071	99
Pan-cancer T cell atlas links a cellular stress response state to immunotherapy resistance. Chu Y, Dai E, Li Y, Han G, Pei G, Ingram DR, Thakkar K, Qin JJ, Dang M, Le X, Hu C, Deng Q, Sinjab A, Gupta P, Wang R, Hao D, Peng F, Yan X, Liu Y, Song S, Zhang S, Heymach JV, Reuben A, Elamin YY, Pizzi MP, Lu Y, Lazcano R, Hu J, Li M, Curran M, Futreal A, Maitra A, Jazaeri AA, Ajani JA, Swanton C, Cheng XD, Abbas HA, Gillison M, Bhat K, Lazar AJ, Green M, Litchfield K, Kadara H, Yee C, Wang L. Nat Med 29: 2023 1550-1562	260
Single-cell chromatin accessibility profiling of acute myeloid leukemia reveals heterogeneous lineage composition upon therapy-resistance. Fan H, Wang F, Zeng A, Murison A, Tomczak K, Hao D, Jelloul FZ, Wang B, Barrodia P, Liang S, Chen K, Wang L, Zhao Z, Rai K, Jain AK, Dick J, Daver N, Futreal A, Abbas HA. Commun Biol 6: 2023 765	10
Accurate identification of locally aneuploid cells by incorporating cytogenetic information in single cell data analysis. Li Z, Li R, Ganan-Gomez I, Abbas HA, Garcia-Manero G, Sun W. Sci Rep 14: 2024 24152	0
A phase I/II trial of WT1-specific TCR gene therapy for patients with acute myeloid leukemia and active disease post-allogeneic hematopoietic cell transplantation: skewing towards NK-like phenotype impairs T cell function and persistence. Mazziotta F, Martin LE, Egan DN, Bar M, Kinsella S, Paulson KG, Voillet V, Lahman MC, Hunter D, Schmitt TM, Duerkopp N, Yeung CCS, Tang TH, Gottardo R, Asano Y, Wilcox EC, Lee B, Zhang T, Lopedote P, Penter L, Wu CJ, Milano F, Greenberg PD, Chapuis AG. Nat Commun 16: 2025 5214	1
A pan-disease and population-level single-cell TCRαβ repertoire reference. Xue Z, Wu L, Gao B, Tian R, Chen Y, Qi Y, Dong T, Bai Y, Zhao Y, He B, Wang L, Liu Z, Yao J, Lu L, Liu W. Cell Discov 11: 2025 82	0