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Expression data from C57/Bl6 Wt mice CD4+ T cells after activation with anti-CD3 plus Wt APC or OX40L-Tg APC

ABSTRACT: Expression data from C57/Bl6 Wt mice CD4+ T cells after activation with anti-CD3 plus Wt APC or OX40L-Tg APC

PROVIDER: PRJNA413298 | ENA |

REPOSITORIES: ENA

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Expression data from C57/Bl6 Wt mice CD4+ T cells after activation with anti-CD3 plus Wt APC or OX40L-Tg APC

Project description:OX40 is a T cell costimulatory molecule in the tumor necrosis factor receptor (TNFR) superfamily. Unlike other costimulatory molecules, OX40 is not expressed by naive T cells, but its expression is rapidly induced following T cell activation, and OX40 costimulation plays a critical role in cell survival, proliferation, and generation of memory cells. We used microarrays to detail the global programme of gene expression of activated CD4 T cells underlying OX40 costimulation and identified distinct classes of up-regulated genes after OX40 costimulation.

2018-05-15 | GSE104611 | GEO

RNA-seq analysis of mTOR{delta}APC and WT lung and spleen APC subsets

Project description:Purified CD11b+, Alveolar macrophage and HDM induced inflammatory DCs from WT and mTOR{delta} APC mice were profiled by RNA-seq to understand mTOR-dependent gene expression

2020-06-20 | GSE100316 | GEO

Apc-mutants act as supercompetitors in intestinal tumour initiation

Project description:Almost all colorectal cancers (CRC) present with mutations in the Apc gene, leading to unrestrained Wnt activation and the initiation of tumour development. We previously reported the competitive benefit of Apc-mutant intestinal stem cells (ISCs) within the crypt, however, the mechanism by which they outcompete their wild type (WT) neighbours remained elusive. Here, we studied the effect of Apc-mutants using an in vitro culture system of WT (Lgr5-CreErt2) and Apc-/- (Lgr5-CreErt2;Apcfl/fl) organoids . The expression patterns of WT and Apc-/- organoids revealed significant upregulation in specific secreted Wnt antagonists Notum, Wif1 and Dkk2. Furthermore, we studied the effect of the secreted antagonist by treating WT organoids with either WT or Apc-/- conditioned medium (CM) for 48 hours and observed a significant decrease in stem cell markers and an increase in goblet cell markers. We report that Apc-mutants act as bona fide supercompetitors by secreting Wnt antagonists that result in active differentiation of WT ISCs.

2021-03-25 | GSE144325 | GEO

Synthetic Essentiality of Tryptophan 2,3-dioxygenase 2 in APC-Mutated Colorectal Cancer II

Project description:Comparative transcriptomic analysis of TAMs isolated from APC-WT and APC-KO MC38 orthotopic tumors express higher levels of multiple classical M2-like markers (CD163, CCL22, YM1) compared to APC-WT tumors after re-normalized the read counts of multiple M2 macrophage markers with housekeeping gene read counts (GAPDH and ACTB).

2022-07-13 | GSE200909 | GEO

Gene expression analysis of WT, Apc and ApcKras mouse intestine

Project description:Gene expression analysis of WT, Apc and ApcKras mouse intestine

| PRJNA673352 | ENA

Transcription profiling of transition from normal intestinal epithelia to adenomas and carcinomas in the APC(Min/+) mice to identify differentially expressed transcripts.

Project description:Transcriptional Profiling of the Transition from Normal Intestinal Epithelia to Adenomas and Carcinomas in the APC(Min/+) Mouse. Samples used in analysis:; * GSM6191-GSM6196 (WT): Ilea epithelial cells from C57/BL6 wild-type samples; * GSM6197-GSM6201 (Adenoma): Epithelial cells from crypts of adenomas of APC(Min/+) mice; * GSM6202-GSM6206 (Carcinoma): Epithelial cells from crypts of carcinomas of APC(Min/+) mice; Using a PixCell IIe instrument (Arcturus), ~30,000 laser firings per sample were used to collect cells of interest. RNA was extracted from captured cells by PicoPure (Arcturus) technique, followed by 2 rounds of RiboAmp amplification (Arcturus), with incorporation of biotinylated nucleotides (Enzo) in the IVT of round 2. All protocols were as per manufacturers instructions. 15ug of labeled cRNA from individual samples were hybridized to respective MG_U74Av2 chips (Affymetrix) and washed/stained using the standard EukGEWS2v4 protocol (Affymetrix). Chips were scanned and analyzed using MAS 5 (Affymetrix) and data scaled to TI=500. Pairwise comparisons using the Mann-Whitney test were performed in DMT 3 (Affymetrix), comparing WT vs Adenoma (n=6 x n=5; 83.3% concordance); WT vs Carcinoma (n=5 x n=5; 84% concordance); Adenoma vs Carcinoma (n=5 x n=5; 84% concordance). This resulted in the identification of differentially expressed transcripts. Fold changes were calculated from signal-log-ratios. Identified transcripts were clustered based on functional information which was publicly available at time of analysis, obtained through the NetAffx web portal (Affymetrix).

2007-11-06 | E-GEOD-422 | biostudies-arrayexpress

Synthetic Essentiality of Tryptophan 2,3-dioxygenase 2 in APC-Mutated Colorectal Cancer I

Project description:We examined the pathways that are regulated by TDO2 in APC-deficient cancer cells by analyzing gene expression profiles of APC-WT and APC-KO MC38 cells that are transduced with inducible shTDO2 constructs. This study establishs that the TDO2-Kyn-AhR axis serves a critical role in promoting APC-deficient tumor growth via cancer cell autonomous (metabolism and proliferation) and non-autonomous mechanisms (tumor immunity).

2022-07-13 | GSE200908 | GEO

Synthetic Essentiality of Tryptophan 2,3-dioxygenase 2 in APC-Mutated Colorectal Cancer [array]

2022-07-13 | GSE201415 | GEO

Synthetic Essentiality of Tryptophan 2,3-dioxygenase 2 in APC-Mutated Colorectal Cancer [ChIP-Seq]

2022-07-13 | GSE201414 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type APC and OX40L-TG APC induced T helper 17 cell Transcriptomes [RNA-seq]

Project description:Purpose:The goals of this study are to evaluate the effect of OX40 ligation on transcriptome profiling of in vitro polarized T helper 17 cell (RNA-seq). Methods: mRNA profiles of CD4+ T cells cultured in vitro under Th17-polarizing conditions for 48hrs (both Ctrl and OX40L treated groups) were generated by deep sequencing, using Illumina RapidRun. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) and TopHat followed by CuffDiff. qRT–PCR validation was performed using SYBR Green assays Results: Among the 398 genes that were significantly affected by OX40, only about 11% were previously identified as RORγt target genes in Th17 cells. Conclusions: Our study suggests that OX40 unlikely affects Th17 commitment, but most likely impairs their effector differentiation. As IL-17A and IL-17F are Th17-defining cytokines, their suppression suggests that OX40 may inhibits effector functions of Th17 cells.

2016-10-06 | GSE80010 | GEO

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