GEO DataSets

(Submitter supplied) Renca, a murine renal cell carcinoma, and B16F10, a murine melanoma, were transcriptionally profiled in a study designed to accompany an in vivo CRISPR screen to identify novel immunotherapy dependencies.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

5 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL19057

35 Samples

Download data

(Submitter supplied) Investigation of the transcriptional response in Jak1 depleted tumor cells upon NK-derived cytokine presence using 3’ RNA sequencing

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

24 Samples

Download data: TXT

(Submitter supplied) Investigation of tumor genes which are involved in the upregulation of MHC I expression through a genome-wide in vitro CRISPR/Cas9 screen

Organism:

Mus musculus

Type:

Other

Platform:

GPL19057

2 Samples

Download data: TXT

(Submitter supplied) Investigation of tumor genes which limit sensitivity to killing by NK cells through a genome-wide in vitro CRISPR/Cas9 screen

Organism:

Mus musculus

Type:

Other

Platform:

GPL19057

3 Samples

Download data: TXT

(Submitter supplied) Investigation of the tumor transcriptional response upon NK cell attack using 3’ RNA sequencing

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: TXT

(Submitter supplied) Single cell transcriptomes of CD45+ cells from KPC tumor subcutaneous allografts, either treated with PD-1+CTLA-4 checkpoint blockade or treatment-naïve.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

8 Samples

Download data: H5

(Submitter supplied) To measure the transcriptomic changes in response to IFNb and IFNg stimulation, we collected RNAseq of various cell lines that were stimulated or unstimulated by interferon for 48 hours

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

70 Samples

Download data: TXT

(Submitter supplied) We adapted pooled non-viral targeted knock-ins to allow for simultaneous readouts of pooled knock-in barcode as well as RNA transcriptomes at the single cell level in primary human T cells. We used a library of 36 potentially therapeutic knock-in constructs each knocked into the TRAC locus along with a new TCR specificity to explore transcriptional changes in therapeutically relvant in vitro and in vivo environments.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

44 Samples

Download data: TAR, TSV

(Submitter supplied) We adapted sgRNA lentiviral infection and Cas9 electroporation (SLICE) to allow for CROP-Seq (Datlinger et al, Nat Med 2017) in primary cells. We used a library of 48 sgRNA, derived from GW screens, to explore transcriptional changes downstream of CRISPR-KO.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

8 Samples

Download data: CSV, TAR

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21103 GPL13112

10 Samples

Download data

(Submitter supplied) CD8+ cytotoxic T cells play essential roles in anti-tumor immune responses. Here, we performed in vivo screens in CD8+ T cells and identified regulators of tumor infiltration and killing, which are directly relevant to cancer immunotherapy. Unlike in vitro screens, the in vivo screen robustly re-identified canonical immunotherapy targets such as PD-1 and Tim-3, along with genes that have not been characterized in T cells. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

2 Samples

Download data: TXT

(Submitter supplied) CD8+ cytotoxic T cells play essential roles in anti-tumor immune responses. Here, we performed in vivo screens in CD8+ T cells and identified regulators of tumor infiltration and killing, which are directly relevant to cancer immunotherapy. Unlike in vitro screens, the in vivo screen robustly re-identified canonical immunotherapy targets such as PD-1 and Tim-3, along with genes that have not been characterized in T cells. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

8 Samples

Download data: TXT

(Submitter supplied) The anti-leukemia activity of NK cells helps to prevent relapse during hematopoietic stem cell transplantation in leukemia patients. However, the factors that determine sensitivity or resistance of leukemia cells in the context of NK-mediated cytotoxicity are not well established. Here we performed a genome-wide CRIPSR screen in the human chronic-myelogenous-leukemia (CML) cell line K562 to identify genes that regulate vulnerability of leukemia cells to killing by primary human NK cells. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

7 Samples

Download data: TXT

(Submitter supplied) By utilizing a simple, modular CRISPR/Cas9 assisted-recombinant vaccinia virus engineering (CARVE) system, we demonstrate generation of a recombinant vaccinia virus expressing three distinct transgenes at three different loci in less than 1 week. This novel vector, STINGPOX, produces cyclic di-AMP, a STING agonist, which drives IFN signaling critical to the anti-tumor immune response.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

4 Samples

Download data: TXT

(Submitter supplied) PTPN2 was deleted from a selection of murine and human cancer cells using CRISPR/Cas9. The loss-of-function phenotype was assessed in vitro with cytokine stimulation or vehicle control.

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21697 GPL21626

81 Samples

Download data: TXT

(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

Platforms:

GPL17021 GPL24247

18 Samples

Download data: NARROWPEAK, TSV

(Submitter supplied) Immune checkpoint blockade (ICB) has shown remarkable clinical efficacy across multiple cancer types. However, only a fraction of patients respond to ICB. Here, we performed pooled mutagenic screening with CRISPR-mediated genetically engineered mouse models (CRISPR-GEMMs) in ICB settings, and identified KMT2D as a major modulator of ICB response across multiple cancer types. Kmt2d encodes a histone H3K4 methyltransferase and is among the most frequently mutated genes in cancer patients. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

12 Samples

Download data: NARROWPEAK, TXT

(Submitter supplied) Immune checkpoint blockade (ICB) has shown remarkable clinical efficacy across multiple cancer types. However, only a fraction of patients respond to ICB. Here, we performed pooled mutagenic screening with CRISPR-mediated genetically engineered mouse models (CRISPR-GEMMs) in ICB settings, and identified KMT2D as a major modulator of ICB response across multiple cancer types. Kmt2d encodes a histone H3K4 methyltransferase and is among the most frequently mutated genes in cancer patients. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: TSV, TXT

(Submitter supplied) We established a direct in vivo CRISPR/Cas9 gene editing methodology that allowed us to assess the immune-modulatory capabilities of 573 putative cancer genes associated with altered activity in mouse model of lung cancer. Using mouse models of of KrasG12D- and BrafV600E-driven lung cancer, we identified Serpinb9 as our top suppressive and Adam2 as our top enhancing gene. RNA seq analysis from tumors overexpressing Adam2 revealed that Adam2’s oncogenic function is dependent on modulating the tumor immune microenvironment by restraining productive type I and type II interferon responses as well as cytokine signaling, reducing presentation of tumor associated antigen, and modulating surface expression of several immunoregulatory receptors within Kras-driven lung tumors. Adam2 overexpression also led to reduction in expression of immune checkpoint inhibitors such as PD-L1, Lag3, Tigit, and Tim3.This less exhausted tumor microenvironment further induced enhanced cytotoxic efficacy against Adam2 overexpressing lung tumors, in vitro and in vivo. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21493

12 Samples

Download data: TXT