@ikohane provided a reference of annotated single cell studies. Here are some titles that look like they might be useful for validation of drug matching (either because of possible drug application or genetic perturbation - bold looked more promising):
Sexual Cell-Fate Reprogramming in the Ovary by DMRT1
Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells
Single-cell based elucidation of molecularly-distinct glioblastoma states and drug sensitivity
CD5L/AIM Regulates Lipid Biosynthesis and Restrains Th17 Cell Pathogenicity
DNMT3A Haploinsufficiency Transforms FLT3ITD Myeloproliferative Disease into a Rapid, Spontaneous, and Fully Penetrant Acute Myeloid Leukemia
Two FGFRL-Wnt circuits organize the planarian anteroposterior axis
HER2 expression identifies dynamic functional states within circulating breast cancer cells
Protein C receptor (PROCR) is a negative regulator of Th17 pathogenicity
Opposing Development of Cytotoxic and Follicular Helper CD4 T Cells Controlled by the TCF-1-Bcl6 Nexus
Deletion of the Polycomb-Group Protein EZH2 Leads to Compromised Self-Renewal and Differentiation Defects in Human Embryonic Stem Cells
Partial exhaustion of CD8 T cells and clinical response to teplizumab in new-onset type 1 diabetes
A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response
Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq
Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens
Engineered Murine HSCs Reconstitute Multi-lineage Hematopoiesis and Adaptive Immunity
Pooled CRISPR screening with single-cell transcriptome readout
Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq
168] Measuring Signaling and RNA-Seq in the Same Cell Links Gene Expression to Dynamic Patterns of NF-κB Activation
IFNγ-Dependent Tissue-Immune Homeostasis Is Co-opted in the Tumor Microenvironment
IL-6/Stat3-Dependent Induction of a Distinct, Obesity-Associated NK Cell Subpopulation Deteriorates Energy and Glucose Homeostasis
Single cardiomyocyte nuclear transcriptomes reveal a lincRNA-regulated de-differentiation and cell cycle stress-response in vivo
IL-11 is a crucial determinant of cardiovascular fibrosis
Erratum: The neuropeptide NMU amplifies ILC2-driven allergic lung inflammation
YY1 Is a Structural Regulator of Enhancer-Promoter Loops
A single-cell hematopoietic landscape resolves 8 lineage trajectories and defects in Kit mutant mice
HMGB2 Loss upon Senescence Entry Disrupts Genomic Organization and Induces CTCF Clustering across Cell Types
Monocyte-derived IL-1 and IL-6 are differentially required for cytokine-release syndrome and neurotoxicity due to CAR T cells
Metabolic regulation of pluripotency and germ cell fate through α‐ketoglutarate
Single-cell analysis of Crohn’s disease lesions identifies a pathogenic cellular module associated with resistance to anti-TNF therapy
Single cell RNA-seq study of wild type and Hox9,10,11 mutant developing uterus
Chromatin mapping and single-cell immune profiling define the temporal dynamics of ibrutinib drug response in chronic lymphocytic leukemia
Ethanol Exposure Increases miR‐140 in Extracellular Vesicles: Implications for Fetal Neural Stem Cell Proliferation and Maturation
Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells
Single cell transcriptomics reveals opioid usage evokes widespread suppression of antiviral genes
Single-cell Transcriptome Mapping Identifies Common and Cell-type Specific Genes Affected by Acute Delta9-tetrahydrocannabinol in Humans
Thyroid hormone regulates distinct paths to maturation in pigment cell lineages
A cellular atlas of Pitx2-dependent cardiac development
Sensory lesioning induces microglial synapse elimination via ADAM10 and fractalkine signaling
Single-cell based elucidation of molecularly-distinct glioblastoma states and drug sensitivity
Lipid-Associated Macrophages Control Metabolic Homeostasis in a Trem2-Dependent Manner
Proteomics and single-cell RNA analysis of Akap4-knockout mice model confirm indispensable role of Akap4 in spermatogenesis
Clonal replacement of tumor-specific T cells following PD-1 blockade
A single-cell transcriptomics CRISPR-activation screen identifies new epigenetic regulators of zygotic genome activation
Single-cell transcriptomic reconstruction reveals cell cycle and multi-lineage differentiation defects in Bcl11a-deficient hematopoietic stem cells
Inhibition of DYRK1A and GSK3B induces human β-cell proliferation
Application of single-cell RNA sequencing in optimizing a combinatorial therapeutic strategy in metastatic renal cell carcinoma
Synergistic Immunostimulatory Effects and Therapeutic Benefit of Combined Histone Deacetylase and Bromodomain Inhibition in Non–Small Cell Lung Cancer
Aging increases cell-to-cell transcriptional variability upon immune stimulation
Generation of Single-Cell Transcript Variability by Repression
Treg Cells Promote the SREBP1-Dependent Metabolic Fitness of Tumor-Promoting Macrophages via Repression of CD8+ T Cell-Derived Interferon-γ
Here are some other studies that caught my eye for one reason or another while looking for possible validation studies
IBD related:
Rewiring of the cellular and inter-cellular landscape of the human colon during ulcerative colitis
Single-cell analysis of Crohn’s disease lesions identifies a pathogenic cellular module associated with resistance to anti-TNF therapy
Colonic epithelial cell diversity in health and inflammatory bowel disease
Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease
Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis
Cryopreservation issue came up with one of Weizmann patients:
DMSO cryopreservation is the method of choice to preserve cells for droplet-based single-cell RNA sequencing
Single-cell transcriptome conservation in cryopreserved cells and tissues
Cell fixation and preservation for droplet-based single-cell transcriptomics
Other interesting:
Bayesian Correlation is a robust similarity measure for single cell RNA-seq data
Accounting for technical noise in single-cell RNA-seq experiments
Integrated genome and transcriptome sequencing of the same cell
Quantification of cell identity from single-cell gene expression profiles
Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons
Massive and parallel expression profiling using microarrayed single-cell sequencing
Batch effects and the effective design of single-cell gene expression studies
Detecting Activated Cell Populations Using Single-Cell RNA-Seq
Single-cell analysis uncovers convergence of cell identities during axolotl limb regeneration
Transcriptomic landscape of the blastema niche in regenerating adult axolotl limbs at single-cell resolution
Advantages of Single-Nucleus over Single-Cell RNA Sequencing of Adult Kidney: Rare Cell Types and Novel Cell States Revealed in Fibrosis
Direct Comparative Analysis of 10X Genomics Chromium and Smart-seq2
Longitudinal single cell transcriptomics reveals Krt8+ alveolar epithelial progenitors in lung regeneration
Aging:
Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells
Intrinsic Age-Dependent Changes and Cell-Cell Contacts Regulate Nephron Progenitor Lifespan
Single-cell RNA sequencing reveals molecular and functional platelet bias of aged haematopoietic stem cells
Progressive alterations in multipotent hematopoietic progenitors underlie lymphoid cell loss in aging
Primary Cell Culture of Live Neurosurgically Resected Aged Adult Human Brain Cells and Single Cell Transcriptomics
Aging increases cell-to-cell transcriptional variability upon immune stimulation
Cell type-specific role of lamin-B1 and its inflammation-driven reduction in organ building and aging
An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics
Quiescence Modulates Stem Cell Maintenance and Regenerative Capacity in the Aging Brain
A cellular and spatial map of the choroid plexus across brain ventricles and ages
Single-cell transcriptomes of the aging human skin reveal loss of fibroblast priming
Mitochondrial dysfunction and endoplasmic reticulum stress involved in oocyte aging: an analysis using single-cell RNA-sequencing of mouse oocytes
Single-cell analysis reveals T cell infiltration in old neurogenic niches
TNF-alpha driven inflammation and mitochondrial dysfunction define the platelet hyperreactivity of aging
IL ‐7‐dependent compositional changes within the γδ T cell pool in lymph nodes during ageing lead to an unbalanced anti‐tumour response
@ikohane provided a reference of annotated single cell studies. Here are some titles that look like they might be useful for validation of drug matching (either because of possible drug application or genetic perturbation - bold looked more promising):
Here are some other studies that caught my eye for one reason or another while looking for possible validation studies
IBD related:
Cryopreservation issue came up with one of Weizmann patients:
Other interesting:
Aging: