GEO DataSets

(Submitter supplied) Myeloid sarcoma is an aggressive extramedullary presentation of acute myeloid leukemia (AML) that may occur with or without medullary involvement. Here, we provide the first comprehensive profiling of myeloid sarcoma. We performed bulk RNA- and DNA-sequencing, as well as single-cell and spatial transcriptomic sequencing of myeloid sarcoma and AML with or without extramedullary disease (EMD), and show that EMD evolves from a pre-existing parental clone in the bone marrow (BM), is driven by increased clonal complexity and tumor mutation burden, and is enriched for RAS pathway mutations compared with AML. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

108 Samples

Download data: COV

(Submitter supplied) Myogenesis is a highly orchestrated process whereby muscle precursor cells, myoblasts, develop into muscle fibers to form skeletal muscle during embryogenesis and regenerate adult muscle. Here, we studied the RNA-binding protein FUS (fused in sarcoma), which has been implicated in muscular and neuromuscular pathologies but is poorly characterized in myogenesis. Given that FUS levels declined in human and mouse models of skeletal myogenesis, and that silencing FUS enhanced myogenesis, we hypothesized that FUS might be a repressor of myogenic differentiation. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL24247

9 Samples

Download data: TXT

(Submitter supplied) Myogenesis is a highly orchestrated process whereby muscle precursor cells, myoblasts, develop into muscle fibers to form skeletal muscle during embryogenesis and regenerate adult muscle. Here, we studied the RNA-binding protein FUS (fused in sarcoma), which has been implicated in muscular and neuromuscular pathologies but is poorly characterized in myogenesis. Given that FUS levels declined in human and mouse models of skeletal myogenesis, and that silencing FUS enhanced myogenesis, we hypothesized that FUS might be a repressor of myogenic differentiation. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

12 Samples

Download data: TXT

(Submitter supplied) Most kidney transplant patients who undergo biopsies are classified as having no rejection based on consensus thresholds. However, we hypothesized that because these patients have normal adaptive immune systems, T cell-mediated rejection (TCMR) and antibody-mediated rejection (ABMR) may exist as subthreshold activity in some transplants currently classified as no rejection. Subthreshold molecular TCMR and/or ABMR activity molecular activity was detectable as elevated classifier scores in many biopsies classified as no rejection, with ABMR activity in many TCMR biopsies and TCMR activity in many ABMR biopsies. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13667

5086 Samples

Download data: CEL, TXT

(Submitter supplied) We examined the phenotypes and functions of SARS-CoV-2-specific T cells in the nasal mucosa of vaccinated individuals with breakthrough infection (BTI) or without infection.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

13 Samples

Download data: H5

(Submitter supplied) The aim of this study is to investigate the specific pathway involved in HLA sensitization using single-cell RNA sequencing analysis and an allo-sensitized mouse model developed with an HLA.A2 transgenic mouse. For sensitization, wild-type C57BL/6 mouse received two skin grafts from C57BL/6-Tg (HLA-A2.1)1Enge/J mouse (allogeneic mouse (ALLO)). For syngeneic control (SYN), skin grafts were transferred from C57BL/6 to C57BL/6. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

2 Samples

Download data: MTX, TSV

(Submitter supplied) The incidence of Mycobacterium avium complex (MAC)-induced pulmonary disease (PD) has been increasing in South Korea, posing considerable challenges in treatment. Treatment guidelines recommend initiating therapy after serial computed tomography (CT) monitoring. While drug treatment often improves outcomes in patients with the nodular bronchiectatic (NB) form, those with the fibrocavitary (FC) form may continue to experience persistence despite treatment. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

42 Samples

Download data: XLSX

(Submitter supplied) PI3K-d inhibitors have shown impressive activity in lymphoid malignancies but have been hampered by autoimmune and infectious toxicities leading to market withdrawals. We previously demonstrated single-agent activity of the PI3K-dg duvelisib in T-cell lymphomas that was associated with inflammatory adverse events. We conducted a phase Ib/IIa study of duvelisib in combination with either romidepsin or bortezomib in patients with relapsed/refractory TCL and found that the addition of romidepsin, but not bortezomib, appeared to increase efficacy while attenuating PI3K inhibitor-driven toxicity. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24676

6 Samples

Download data: CSV

(Submitter supplied) Gigaxonin, the GAN gene product, is a E3 ubiquitin ligase adaptor and is involved in neural cell and fibroblast intermediate filament processing. We have previously shown that gigaxonin in association with p16 ubiquitinates NF-κB in head and neck cancer. The cancer genomic database search has shown higher frequency of GAN gene exon 8 single nucleotide polymorphism (SNP, rs2608555), c.1293 C>T, p.Y431Y, in the normal Caucasian population (44.25% vs <20% in other populations). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

4 Samples

Download data: CSV

(Submitter supplied) 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:

GPL24247

24 Samples

Download data: BW

(Submitter supplied) Foxp3low inflammatory non-suppressive (INS)-regulatory T cells (Tregs) were discovered recently. Unlike conventional Tregs, they produce proinflammatory-cytokines, exhibit reduced suppressiveness, and promote rather than impair anti-tumor immunity. The role of mitochondria in Foxp3low INS-Treg formation in vivo is unclear. We showed that the Foxp3low INS-Treg equivalents in human tumors demonstrate attenuated expression of CRIF1, a vital mitochondrial regulator. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

16 Samples

Download data: BED, BW

(Submitter supplied) Foxp3low inflammatory non-suppressive (INS)-regulatory T cells (Tregs) were discovered recently. Unlike conventional Tregs, they produce proinflammatory-cytokines, exhibit reduced suppressiveness, and promote rather than impair anti-tumor immunity. The role of mitochondria in Foxp3low INS-Treg formation in vivo is unclear. We showed that the Foxp3low INS-Treg equivalents in human tumors demonstrate attenuated expression of CRIF1, a vital mitochondrial regulator. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

8 Samples

Download data: TXT

(Submitter supplied) As training dataset for Random Promoter DREAM Challenge 2022, we generated ~6.7 million synthetic promoters (in yeast) comprised of random DNA (N80) and measured their expression by FACS (sorting into 18 bins). As test dataset for Random Promoter DREAM Challenge 2022, we generated ~71k synthetic promoters (in yeast) comprised of designed DNA (NBT) and measured their expression by FACS (sorting into 18 bins).

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL19756

36 Samples

Download data: TXT

(Submitter supplied) Intrahepatic cholangiocarcinoma (ICC) has limited therapeutic options and a dismal prognosis. Adding blockade of the PD1 pathway to gemcitabine/cisplatin chemotherapy has recently shown efficacy in biliary tract cancers but with low response rates. Here, we studied the effects of anti-CTLA-4 when combined with anti-PD1 and gemcitabine/cisplatin in orthotopic murine models of ICC. This combination therapy led to substantial survival benefits and reduction of morbidity in two aggressive ICC models that were resistant to immunotherapy alone. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30172

8 Samples

Download data: CSV, RDS

(Submitter supplied) Intrahepatic cholangiocarcinoma (ICC) has limited therapeutic options and a dismal prognosis. Adding blockade of the PD1 pathway to gemcitabine/cisplatin chemotherapy has recently shown efficacy in biliary tract cancers but with low response rates. Here, we studied the effects of anti-CTLA-4 when combined with anti-PD1 and gemcitabine/cisplatin in orthotopic murine models of ICC. This combination therapy led to substantial survival benefits and reduction of morbidity in two aggressive ICC models that were resistant to immunotherapy alone. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

12 Samples

Download data: TXT

(Submitter supplied) Microbes are an integral component of the tumor microenvironment (TME). However, mechanisms that direct microbial recruitment into tumors and the spatial relationship between intratumoral microbes and host cells remain poorly understood. Here, we show that microbes and immune cells have parallel spatial distribution and that the presence of intratumoral microbes is dependent on T cells. Analysis of human pancreatic ductal adenocarcinomas (PDAC) and lung adenocarcinomas (LUAD) revealed a spatially heterogeneous distribution of lipopolysaccharide (LPS) that is associated with T cell infiltration. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

16 Samples

Download data: TXT

(Submitter supplied) Solid tumors are composed of cancer cells and host immune cells that are distributed in a non-uniform pattern. Growing evidence shows that intratumoral microbes are associated with immune microenvironments in cancer. However, mechanisms that direct the recruitment of microbes to tumors remain poorly understood. Here, we show that intratumoral infiltration of immune cells and microbes are heterogeneous, and the distribution of microbes within tumors are orchestrated by the spatial heterogeneity of intratumoral lymphoid populations. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

12 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL19057

57 Samples

Download data

(Submitter supplied) Solid tumors are composed of cancer cells and host immune cells that are distributed in a non-uniform pattern. Although this spatial heterogeneity may reflect mutational variations in cancer cells, mechanisms that direct the recruitment of immune cells to distinct regions within a tumor remain poorly understood. Here, we show that microbial-host interactions define tumor nests enriched in immune cells, and the distribution of microbes within tumors parallels the spatial heterogeneity of intratumoral lymphoid and myeloid cell populations. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

20 Samples

Download data: TXT

(Submitter supplied) Solid tumors are composed of cancer cells and host immune cells that are distributed in a non-uniform pattern. Although this spatial heterogeneity may reflect mutational variations in cancer cells, mechanisms that direct the recruitment of immune cells to distinct regions within a tumor remain poorly understood. Here, we show that microbial-host interactions define tumor nests enriched in immune cells, and the distribution of microbes within tumors parallels the spatial heterogeneity of intratumoral lymphoid and myeloid cell populations. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

16 Samples

Download data: TXT