High-content Datasets

We are committed to providing public access to high-quality high-content datasets generated in the laboratory. Links below provide access to deposited high-throughput sequencing datasets generated by the laboratory through our primary and collaborative work.

BACH2 is repurposed following Treg lineage commitment to drive the functional quiescence and maintenance of resting Treg cells

In various tissues, cellular homeostasis is achieved by functionally quiescent stem cells which self renew while giving rise to differentiated progeny. Regulatory T (Treg) cells are composed of functionally quiescent resting Treg (rTreg) cells which differentiate into activated Treg (aTreg) cells upon antigen stimulation. How rTreg cells remain quiescent despite chronic exposure to cognate self- and foreign antigens is unclear. more…

Organism: Mus musculus

Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms: GPL13112 GPL21103 GPL17021 

23 Samples

Download data: BED, NARROWPEAK

Accession: GSE128176; ID: 200128176

 

Single-cell RNA-Seq analysis of WT and Bach2-deficient Foxp3+ Treg cells

These are the FastQ files used for scRNA-Seq analysis of WT and Bach2-deficient splenic Foxp3+ Treg cells

Organism: Mus musculus

Type: Expression profiling by high throughput sequencing

Platform: GPL21103 

6 Samples

Download data: CSV, XLSX

Accession: GSE128175 ID: 200128175

 

Bulk RNA-Seq analysis of WT and Bach2-deficient Foxp3+ Treg cells

These are the FastQ files used for the RNA-seq analysis of WT and Bach2-deficient splenic Foxp3+ Treg cells.

Organism: Mus musculus

Type: Expression profiling by high throughput sequencing

Platform: GPL17021 

6 Samples

Download data: TXT

Accession: GSE127699 ID: 200127699

 

Heterogeneous Bach2 expression distinguishes rTreg cells and aTreg cells

These are the FastQ files used for RNA-Seq analysis of splenic Foxp3+ Treg cells that express either high or low levels of Bach2

Organism: Mus musculus

Type: Expression profiling by high throughput sequencing

Platform: GPL17021 

8 Samples

Download data: TXT

Accession: GSE127698 ID: 200127698

 

Distribution of genome-wide BACH2 or JunD binding sites identified by ChIP-Seq in iTreg cells

In various tissues, cellular homeostasis is achieved by functionally quiescent stem cells which selfrenew while giving rise to differentiated progeny. Regulatory T (Treg) cells are composed of functionally quiescent resting Treg (rTreg) cells which differentiate into activated Treg (aTreg) cells upon antigen stimulation. How rTreg cells remain quiescent despite chronic exposure to cognate self- and foreign antigens is unclear. more…

Organism: Mus musculus

Type: Genome binding/occupancy profiling by high throughput sequencing

Platform: GPL13112 

3 Samples

Download data: BED, NARROWPEAK

Accession: GSE127695 ID: 200127695

 

High-dimensional single cell analysis reveals an effector Treg molecular program that correlates with lung cancer progression

Anti-tumor immune responses are counteracted by CD4+ regulatory T (Treg) cells in the tumor micronenvironment, but the molecular mechanisms responsible for the enhanced suppressive activity of Tregs are poorly defined. High-dimensional single cell profiling of millions of single CD4+ and CD8+ T cells from 53 chemotherapy-na‹ve individuals with lung adenocarcinoma identified the transcription factor IRF4 as constitutively expressed by effector CD4+ Tregs present exclusively in tumors. more…

Organism: Homo sapiens

Type: Expression profiling by high throughput sequencing

Platform: GPL18573 

10 Samples

Download data: CSV

Accession: GSE128822 ID: 200128822

 

The 11q13.5 immune disease risk locus contains a distal enhancer required for Treg-mediated suppression of gut inflammation [ATAC-Seq]

Much of the genetic variation underlying susceptibility to common autoimmune and allergic diseases is concentrated within protein non-coding regulatory elements termed enhancers{Enhancer; Hsniz}. It has been difficult to assign functions to a majority of enhancers that overlap immune disease-associated variants due to their distance from the genes they regulate, our lack of understanding of the cell types in which they operate and our inability to recapitulate the biology of immune-mediated diseases in vitro. more…

Organism: Mus musculus

Type: Genome binding/occupancy profiling by high throughput sequencing

Platform: GPL17021 

12 Samples

Download data: BROADPEAK

Accession: GSE143515 ID: 200143515

 

The 11q13.5 immune disease risk locus contains a distal enhancer required for Treg-mediated suppression of gut inflammation [RNA-Seq]

Much of the genetic variation underlying susceptibility to common autoimmune and allergic diseases is concentrated within protein non-coding regulatory elements termed enhancers{Enhancer; Hsniz}. It has been difficult to assign functions to a majority of enhancers that overlap immune disease-associated variants due to their distance from the genes they regulate, our lack of understanding of the cell types in which they operate and our inability to recapitulate the biology of immune-mediated diseases in vitro. more…

Organism: Mus musculus

Type: Expression profiling by high throughput sequencing

Platform: GPL17021 

12 Samples

Download data: TXT

Accession: GSE128198 ID: 200128198

 

The 11q13.5 immune disease risk locus contains a distal enhancer required for Treg-mediated suppression of gut inflammation

This SuperSeries is composed of the SubSeries listed below.

Organism: Mus musculus

Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform: GPL17021 

24 Samples

Download data: BROADPEAK

Accession: GSE143516 ID: 200143516

 

Dysfunction and stemness of tumor-infiltrating T cells are triggered by a common mechanism

The paradox of tumor immunology is that tumor infiltrating lymphocytes (TILs) are dysfunctional in situ and yet are capable of stem cell-like behavior with self-renewal, massive expansion, multipotency, and eradication of large metastatic tumors. Here we report that the overabundance of potassium in the tumor microenvironment (TME) can explain both phenomena.

Organism: Mus musculus

Type: Genome binding/occupancy profiling by high throughput sequencing

Platforms: GPL9185 GPL11002 

10 Samples

Download data: BED, BW

Accession: GSE122156 ID: 200122156

 

The transcription factor Myb enhances CD8+ T cell stemness and antitumor immunity

Stem cells are maintained by transcriptional programs promoting self-renewal and repressing differentiation. Here, we show that the transcription factor Myb is essential for generating and maintaining stem cells within the CD8+ T-cell memory compartment. We found that, following viral infection, CD8+ T cells lacking Myb underwent terminal differentiation and exhibited impaired capacity to form CD62L+ stem cell-like memory cells. more…

Organism: Mus musculus

Type: Expression profiling by high throughput sequencing

Platform: GPL9185 

6 Samples

Download data: TXT

Accession: GSE112049 ID: 200112049

 

Probing Hemogenic Precursors with Endoglin Regulatory Elements uncovers LRP2 as a Regulator of Hematopoiesis

Different combinations of Endoglin tissue specific enhancers define hemangioblast and hemogenic endothelium cell fractions

Organism: Mus musculus

Type:Expression profiling by high throughput sequencing

Platform: GPL13112 

15 Samples

Download data: TXT

Accession: GSE77390 ID: 200077390

 

Ionic immune suppression within the tumour microenvironment limits T cell effector function

Tumours progress despite being infiltrated by effector T cells. Tumour necrosis is associated with poor survival in a variety of cancers. Here, we report that that necrosis causes release of an intracellular ion, potassium, into the extracellular fluid of human and mouse tumours. Surprisingly, elevated extracellular potassium ([K+]e) was sufficient to profoundly suppress mouse and human T cell anti-tumour function. more…

Organism: Mus musculus

Type: Expression profiling by high throughput sequencing

Platform: GPL17021 

12 Samples

Download data: TXT

Accession: GSE84996 ID: 200084996

 

T cell oxygen-sensing proteins establish an immunologically tolerant metastatic niche

Cancer cells must evade immune responses at distant sites to establish metastases. The lung is a frequent site for metastasis. We hypothesized that lung-specific immunoregulatory mechanisms create an immunologically permissive environment for tumor colonization. We found that T cell-intrinsic expression of the oxygen-sensing prolyl-hydroxylase (PHD) proteins is required to maintain local tolerance against innocuous antigens in the lung, but powerfully licenses colonization by circulating tumor cells. more…

Organism: Mus musculus

Type: Expression profiling by high throughput sequencing

Platforms: GPL13112 GPL17021 

18 Samples

Download data: TXT

Accession: GSE85131 ID: 200085131

 

The transcription factor BACH2 is required to establish immunosuppression within tumors

Through a diversity of functional lineages, cells of the innate and adaptive immune system either drive or constrain immune reactions within tumors. Thus, while the immune system has a powerful ability to recognize and kill cancer cells, this function is often suppressed preventing clearance of disease. The transcription factor (TF) BACH2 controls the differentiation and function of multiple innate and adaptive immune lineages, but its role in regulating tumor immunity is not known. more…

Organism: Mus musculus

Type: Expression profiling by array

Platform: GPL1261 

10 Samples

Download data: CEL

Accession: GSE74653 ID: 200074653

 

BACH2 regulates CD8+ T cell differentiation by controlling access of AP-1 factors to enhancers

T cell antigen receptor (TCR) signaling drives distinct responses depending upon the differentiation state and context of CD8+ T cells. We hypothesized that access of signal-dependent transcription factors (TFs) to enhancers is dynamically regulated to shape transcriptional responses to TCR signaling. We found that the TF BACH2 restrains terminal differentiation to enable generation of long-lived memory cells and protective immunity following viral infection. more…

Organism: Mus musculus

Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms: GPL9250 GPL13112 

47 Samples

Download data: BED, TXT

Accession: GSE77857 ID:200077857

 

Mitochondrial Membrane Potential Identifies Cells with Enhanced Stemness for Cellular Therapy

Long-term survival and antitumor immunity of adoptively transferred CD8+ T cells is dependent on their metabolic fitness, but approaches to isolate therapeutic T cells based on metabolic features are not well established. Here we utilized a lipophilic cationic dye tetramethylrhodamine methyl ester (TMRM) to identify and isolate metabolically robust T cells based on their mitochondrial membrane potential (ΔΨm). more…

Organism: Mus musculus

Type: Expression profiling by high throughput sequencing

Platform:  GPL13112 

2 Samples

Download data: TXT

Accession: GSE74001 ID: 200074001

 

Gene expression data from Zeb2WT, Zeb2KO, T-betWT and T-betKO effector CD8+ T cells during infection

ZEB2 is a multi-zinc-finger transcription factor known to play a significant role in early neurogenesis and in EMT-dependent tumor metastasis. While the function of ZEB2 in T lymphocytes is unknown, activity of the closely related family member ZEB1 has been implicated in lymphocyte development. Here, we find that ZEB2 expression is upregulated by activated T cells, specifically in the KLRG1hi effector CD8+ T cell subset. more…

Organism: Mus musculus

Type: Expression profiling by array

Platform: GPL6246 

10 Samples

Download data: CEL

Accession: GSE72162 ID: 200072162

 

Histone architecture of stem-cell memory T cells reveals progressive remodeling of epigenetic landscape after activation of CD8 T cells

To better elucidate epigenetic mechanisms that correlate with the dynamic gene expression program observed after T cell activation, we investigated the genomic landscape of histone modifications in antigen-experienced CD8+ T cells. Using a ChIP-Seq approach coupled with global gene expression profiling, we generated genome-wide histone H3 lysine 4 (H3K4me3) and H3 lysine 27 (H3K27me3) trimethylation maps in distinct subsets of CD8+ T cells-naïve, stem cell memory, central memory, and effector memory-to gain insight into how histone architecture is remodeled during the differentiation of activated T cells. more…

Organism: Mus musculus

Type: Expression profiling by array

Platform:  GPL6246 

12 Samples

Download data: CEL

Accession: GSE67825 ID: 200067825

 

Inhibition of Akt promotes immunologic memory in tumor-infiltrating lymphocytes isolated from patients with melanoma

Adoptive cell immunotherapy (ACT) using autologous tumor-infiltrating lymphocytes (TIL) can result in complete regression of advanced melanoma in some patients, but the efficacy of this potentially curative therapy is limited by poor persistence of TIL after adoptive-transfer. Pharmacologic inhibition of the serine/threonine kinase Akt has recently been shown to promote immunologic memory in viral-specific murine models, but whether this approach may enhance features of memory (e.g. more…

Organism: Homo sapiens

Type: Expression profiling by array

Platform: GPL6244 

24 Samples

Download data: CEL

Accession: GSE60977 ID: 200060977

 

Cish inhibits CD8+ T cell immunity and disrupts proximal T cell receptor signaling

T cell receptor (TCR) signaling is a critical process in immunity to infectious disease and cancer. Recently, a genome-wide association study has implicated polymorphisms in the CISH locus with susceptibility to infectious diseases. However, the role of Cish in the immune responses and its molecular underpinnings remains unclear. Here we demonstrate that Cish deletion resulted in protection against viral infection and enhanced CD8+ T cell tumor immunity. more…

Organism: Mus musculus

Type: Expression profiling by array

Platform: GPL6246 

13 Samples

Download data: CEL

Accession: GSE56328 ID: 200056328

 

The kinase DYRK1A reciprocally regulates the differentiation of Th17 and regulatory T cells [seq]

Using an unbiased chemical biology approach, we discover harmine as a novel regulator of Treg/Th17 differentiation. Harmine enhances Treg differentiation (working in conjunction with low levels of exogenous TGFb) and inhibits Th17 differentiation. Analysis of global gene expression of Tregs generated using low TGFb + harmine reveals significant similarity to Tregs generated using high TGFb only and suggests relevance of harmine-engaged mechanisms to IBD.

Organism: Mus musculus

Type: Expression profiling by high throughput sequencing

Platform: GPL16417 

6 Samples

Download data: MATRIX

Accession: GSE67960 ID: 200067960

 

The kinase DYRK1A reciprocally regulates the differentiation of Th17 and regulatory T cells [array]

Using an unbiased chemical biology approach, we discover harmine as a novel regulator of Treg/Th17 differentiation. Harmine enhances Treg differentiation (working in conjunction with low levels of exogenous TGFb) and inhibits Th17 differentiation. Analysis of global gene expression of Tregs generated using low TGFb + harmine reveals significant similarity to Tregs generated using high TGFb only and suggests relevance of harmine-engaged mechanisms to IBD.

Organism: Mus musculus

Type: Expression profiling by array

Platform: GPL6887 

12 Samples

Download data: TXT

Accession: GSE64247 ID: 200064247

 

Histone architecture of stem-cell memory T cells reveals progressive remodeling of epigenetic landscape in antigen-experienced CD8 T cells

We investigated the genomic landscape of histone modifications in antigen-experienced CD8+ T cells. Using a ChIP-Seq approach coupled with global gene expression profiling [GSE67825], we generated genome-wide histone H3 lysine 4 (H3K4me3) and H3 lysine 27 (H3K27me3) trimethylation maps in distinct subsets of CD8+ T cells - naïve, stem cell memory, central memory, and effector memory.

Organism: Mus musculus

Type: Genome binding/occupancy profiling by high throughput sequencing

Platform: GPL9185 

8 Samples

Download data: WIG

Accession: GSE67881 ID: 200067881

 

Type-1-cytokines synergize with oncogene inhibition to induce tumor growth arrest

Both targeted inhibition of oncogenic driver mutations and immune-based therapies show efficacy in treatment of patients with metastatic cancer but responses are either short-lived or incompletely effective. Oncogene inhibition can augment the efficacy of immune-based therapy but mechanisms by which these two interventions might cooperate are incompletely resolved. Using a novel transplantable BRAFV600E-mutant murine melanoma model (SB-3123), we explore potential mechanisms of synergy between the selective BRAFV600E inhibitor vemurafenib and adoptive cell transfer (ACT)-based immunotherapy. more…

Organism: Mus musculus

Type: Expression profiling by array

Platform: GPL6246 

12 Samples

Download data: CEL

Accession: GSE62249 ID: 200062249

 

Stretch-Enhancers Delineate Disease-Associated Regulatory Nodes in T Cells

T Cell stretch-enhancers are vulnerable to Jak inhibitor tofacitinib

Organism: Homo sapiens; Mus musculus

Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms: GPL9250 GPL13112 GPL11154 

21 Samples

Download data: BW

Accession: GSE60482 ID: 200060482

 

Gene expression in Bach2-deficient and wildtype CD4 single-positive thymocytes from mixed chimeric animals

The role of FoxP3+ regulatory T (Treg) cells in the maintenance of immunological tolerance is well established. Recently, genome-wide association studies (GWAS) in humans have associated polymorphisms within the BACH2 locus encoding the transcription factor BTB and CNC homology 1, basic leucine zipper transcription factor 2 (Bach2) with diverse allergic and autoimmune diseases including asthma, multiple sclerosis, Crohn’s disease, celiac disease, generalized vitiligo and type 1 diabetes. more…

Organism: Mus musculus

Type: Expression profiling by array

Platform:  GPL6246 

6 Samples

Download data: CEL

Accession: GSE42598 ID: 200042598

 

Retinoic acid determines the in vivo fate-commitment of splenic pre-dendritic cells

Comparison of gene expression changes of FACS sorted splenic CD11b+CD8a- and CD11b-CD8a+ cDC subsets reconstituted in vivo following total body irradiation in combination with exogenous retinoic acid or vehicle control.

Organism: Mus musculus

Type: Expression profiling by array

Platform:  GPL6246 

16 Samples

Download data: CEL

Accession: GSE41021 ID: 200041021

 

CD8+ T-cell memory bears the transcriptional imprint of progressive differentiation

The generation of CD8+ T-cell memory is an important aim of immunization. While several distinct subsets of CD8+ T-cell memory have been described, the lineage relationships between effector (EFF), effector memory (EM) and central memory (CM) T cells remain contentious. Specifically, there is contradictory experimental evidence to support both the linear (Naive>EFF>EM>CM) and progressive differentiation (Naive>CM>EM>EFF) models. more…

Organism: Mus musculus

Type: Expression profiling by array

Platform:  GPL8389 

67 Samples

Download data: TXT

Accession: GSE42459 ID: 200042459

 

Bach2 represses effector programmes to stabilize Treg-mediated immune homeostasis

Through their functional diversification, CD4+ T cells play key roles in both driving and constraining immune-mediated pathology. Transcription factors are critical in the generation and maintenance of cellular diversity and negative regulators antagonistic to alternate fates often act in conjunction with positive regulators to stabilize lineage specification1. Polymorphisms within the locus encoding a transcription factor BACH2 are associated with diverse immune-mediated diseases including asthma2, multiple sclerosis3, Crohn¹s disease4-5, coeliac disease6, vitiligo7 and type 1 diabetes8. more…

Organism: Mus musculus

Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform: GPL13112 

12 Samples

Download data: RPKM, TXT, WIG

Accession: GSE45975 ID: 200045975

 

Permissivity of the NCI-60 cancer cell lines to oncolytic Vaccinia Virus GLV-1h68

Oncolytic viral therapy represents an alternative therapeutic strategy for the treatment of cancer. This therapy relies on efficient replication of virus in tumor cells in vivo with minimal or no replication in normal tissues. We recently described GLV-1h68 as a modified Vaccinia Virus (VACV) construct with exclusive in vivo tropism for tumor cells in experimental animal models. Moreover, we had previously observed a cell line-specific relationship between the ability of GLV-1h68 to replicate in vitro during the first 20 hours following infection and the in vivo ability to colonize and eliminate the corresponding tumor implant. more…

Organism: Homo sapiens

Type: Expression profiling by array

Platform: GPL13224 

76 Samples

Download data: TXT

Accession: GSE28472 ID:200028472

 

Expression data from in vitro and ex vivo Th1- and Th17-polarized TRP1 TCR transgenic CD4+ cells

Serial comparison between Th1 and Th17 tumor-specific cells cultured in vitro and ex vivo after transferred into sublethaly irradiated B6.PL mice. Th17-derived cells acquire Th1-like properties in vivo but maintain a distinct molecular profile.

Organism: Mus musculus

Type: Expression profiling by array

Platform: GPL6246 

28 Samples

Download data: CEL]

Accession: GSE26030 ID: 200026030