Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Multifactorial remodeling of the cancer immunopeptidome by interferon gamma

ABSTRACT: In this study we combined previous transcriptomics and immunopeptidomics data with new proteomics data from untreated and IFNg-treated CRC PDOs to dissect mechanisms that lead to remodeling of the immunopeptidome through IFNg treatment (this is from the paper introduction, let me know if it needs any stylistic changes). · Experiment description: The cells were grown in DMEM/F12 media with 20% fetal bovine serum, 1X Glutamax, 100 units/ml penicillin/streptomycin and 2% matrigel, and treated with 600ng/mL IFNg for 48 hours before harvesting. Cells were washed twice with ice-cold PBS then snap-frozen.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: James Wright

LAB HEAD: Jyoti Choudhary

PROVIDER: PXD031634 | Pride | 2023-09-29

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Similar Datasets

Differential proteomic profiling between Cancer Associated Fibroblasts and KRAS mutated cancer cell lines

Project description:Purpose Cancer-associated fibroblasts (CAFs) are a key component of tumors. We aimed to profile the proteome of cancer cell lines representing three common cancer types (lung, colorectal and pancreatic) and a representative CAF cell line from each tumor type to gain insight into CAF function and identify new CAF biomarkers. Experimental Design We used isobaric labeling, liquid chromatography and mass spectrometry to evaluate the proteome of 9 cancer and 3 CAF cell lines. Functions of selected differentially expressed proteins in CAF cell lines were further investigated using siRNA and the expression levels of candidate novel CAF biomarkers were evaluated by immunohistochemistry in 30 human tumor specimens. Results Of the 9460 proteins evaluated, functional enrichment analysis revealed N-glycan biosynthesis and extracellular membrane proteins to be upregulated in CAFs and not in cancer cells. 85 proteins had 16-fold higher expression in CAFs compared to cancer cells. These included previously known CAF markers like ACTA2, FAP and SDC2. Novel biomarkers overexpressed in CAFs were noted, including HSPB6 and PTGS1. SiRNA knockdown of these genes encoding these proteins did not reduce contractility in lung CAFs, suggesting they were not crucial to this function despite high expression. Immunohistochemical analysis of 30 tumor samples (10 lung, 10 colorectal and 10 pancreatic) showed HSPB6 and PTGS1 expression were restricted to the stroma. Conclusions An unbiased analysis of the differences in the proteome of cancer cells compared to CAFs revealed increased expression of HSPB6 and PTGS1 in CAFs.

2023-08-21 | PXD040360 | Pride

Tiling path analysis to map chromatin anchors within the human Major Histocompatability Complex region from B-lymphoblastoid cells and IFNg+/IFNg- treated fibroblasts

Project description:Mapping of chromatin anchors within the human Major Histocompatability Complex (MHC) region from B-lymphoblastoid cells and IFNg+/IFNg- treated fibroblasts.

2008-10-01 | E-MEXP-1793 | biostudies-arrayexpress

Proteomic analysis of Dscc1 knockout mouse cells

Project description:In this project we aimed to explore the effect of Dscc1 gene loss on the proteome. Embyros from wildtype and aged matched Dssc1 null embryos were profiled.

2023-11-17 | PXD034902 | Pride

MG1655 flagellar regulator ChIP-seq (FlhD, FlhC, FliA)

Project description:We mapped the genome-wide binding of the flagellar regulators FlhD, FlhC, and FliA in FLAG-tagged derivatives of E. coli K-12 MG1655 using ChIP coupled with deep sequencing (ChIP-seq). We identify new binding sites for each factor.

2014-04-10 | E-MTAB-2457 | biostudies-arrayexpress

Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding

Project description:We investigated the genome-wide binding sites for sigma54 and RNA polymerase in wild-type Escherichia coli MG1655.

2015-08-06 | E-MTAB-3697 | biostudies-arrayexpress

Chromatin immunoprecipitation of Drosophila DNA to identify nucleosomes bound by RNA polymerase II

Project description:Crosslinked chromatin was digested with Micrococcal nuclease and immunopurified for Rpb3, a subunit of RNA Polyermase II. chIP'd DNA was hybridized to Drosophila tiling arrays and nucleosomes that were bound by Pol II were mapped.

2008-05-20 | E-MEXP-1515 | biostudies-arrayexpress

Salmonella 14028s AraC ChIP-Seq

Project description:We mapped the genome-wide binding of C-terminally FLAG-tagged AraC in S. enterica subsp. enterica serovar Typhimurium strain 14028s using ChIP coupled with deep sequencing (ChIP-seq). We identified five putative target loci for AraC: upstream of araB/araC, araE, araJ, STM14_0178, and within sseD.

2013-10-09 | E-MTAB-1915 | biostudies-arrayexpress

ChIP-seq of sigma 70 in wild-type and hns mutant Escherichia coli K-12 MG1655

Project description:We mapped the genome-wide binding of sigma 70 in E. coli K-12 MG1655 and an hns mutant that is otherwise isogenic using ChIP coupled with deep sequencing (ChIP-seq). We show that intragenic binding of sigma 70 is increased in the hns mutant.

2013-12-15 | E-MTAB-2148 | biostudies-arrayexpress

Binding of the C. elegans dosage compensation complex protein DPY-27

Project description:Dosage Compensation is required to correct for uneven gene dose between the sexes. We utilized global run-on sequencing (GRO-seq) to examine how Caenorhabditis elegans dosage compensation reduces transcription of X-linked genes. To facilitate these experiments, we required accurate 5M-bM-^@M-^Y-ends of genes that have been missing due to a co-transcriptional trans-splicing event common in nematodes. We developed a modified GRO-seq protocol to identify TSSs that are supported by transcription, and determined that TSSs lie more than 1 kb upstream of the previously annotated TSS for nearly one-quarter of all genes. We then investigated the changes that occur in transcriptionally engaged RNA Polymerase when dosage compensation is disrupted, and find that dosage compensation controls recruitment of RNA Polymerase to X-linked genes. Two biological replicates of ChIP with DPY-27 and a random rabbit IgG

2013-06-18 | E-GEOD-43086 | biostudies-arrayexpress

Dissecting psa locus regulation in Yersinia pestis

Project description:We looked at H-NS bound sites in wild type Yersinia pestis and in a mutant strain in which the psaE gene was deleted.

2021-06-01 | E-MTAB-10694 | biostudies-arrayexpress