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RNA-seq analysis of crypt samples isolated from the small intestine of Bach2 KO and control mice

ABSTRACT: RNA-seq analysis of crypt samples isolated from the small intestine of Bach2 KO and control mice

PROVIDER: PRJEB42402 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR5056070_1.fastq.gz	Fastqsanger.gz
	ERR5056070_2.fastq.gz	Fastqsanger.gz
	ERR5056071_1.fastq.gz	Fastqsanger.gz
	ERR5056071_2.fastq.gz	Fastqsanger.gz
	ERR5056066_1.fastq.gz	Fastqsanger.gz

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RNA-seq analysis of crypt samples isolated from the small intestine of Bach2 KO and control mice

Project description:Epithelial regeneration is critical for barrier maintenance and organ function after intestinal injury. Here, we found that Bach2 deficiency promotes the intestinal epithelial cell proliferation during homeostasis and facilitates the crypt regeneration after irradiation, resulting in a reduction of mortality. RNA-seq analysis of isolated crypts revealed that Bach2 deficiency altered expression of numerous genes including those regulating DSBs repair. Crypts were isolated from the small intestines of Bach2 KO and control mice (n=3, respectively) 10 days after tamoxifen administration. Total RNA was extracted for sequencing using RNA-Seq.

2021-01-12 | E-MTAB-9865 | biostudies-arrayexpress

mRNA expression in CD4+ CD25+ GITR+ regulatory T cells from WT and Bach2 KO mice

Project description:Bach2 regulates homeostasis of foxp3+ regulatory T cells and protects against fatal lung disease in mice. Cells from WT and Bach2 KO spleen were isolated. CD4+ CD25+ GITR+ (Treg) cells were sorted by FACS sorting. Total RNAs were extracted from sorted Treg cells using by Rneasy Kit (Qiagen).

2013-11-14 | E-GEOD-52337 | biostudies-arrayexpress

Expression profiles of villus and crypt layers of large intestine from C57Bl/6, Apc1638N+/-, and p21-/- mice.

Project description:Expression profiles obtained from the villus and crypt layers of murine large intestine can elucidate the process of differentiation undergone by epithelial cells as they migrate from the undifferentiated bottom of the crypt to the villus tip before being shed into the intestinal lumen. This series includes profiles from wild type mice, as well as mice harboring mutations in genes (APC and p21) which play key roles in the differentiation process. We used microarrays to characterize gene expression profiles at the base of the crypt and at the villus tip of the lumenal layer of the large intestine in order to better understand the process of differentiation and eventual shedding undergone by cells of the large intestinal epithelium. Four wild type, four APC1638+/- and four p21-/- mice were sacrified and the large intestines dissected out. Cells from the villus tip and from the bottom of the crypt were isolated from the lumenal face of the each large intestine using the Weiser method of sequential elution. RNA was extracted from each eluted sample and used to hybridize to Affymetrix 3' expression arrays.

2010-10-06 | E-GEOD-19338 | biostudies-arrayexpress

Expression profiles of villus and crypt layers of large intestine from C57Bl/6, Apc1638N+/-, and p21-/- mice.

2010-10-06 | GSE19338 | GEO

Expression data from induced pluripotent stem cell-derived crypt-villus structural small intestine

Project description:We established the co-culture model of iPS cell-derived crypt-villus structural small intestine and lactic acid bacteria (LABs). Using this model, the effect of TNF-α, IFN-γ and LABs (Lactobacillus delbrueckii subsp. bulgaricus 2038 and Streptococcus thermophilus 1131) on the cells was evaluated.

2025-03-10 | GSE291253 | GEO

Super-killer CTLs are generated by single gene deletion of Bach2

Project description:Bach2 codes for a transcriptional regulator exerting major influences on T cell mediated immune regulation. Effector CTLs derived from in vitro activation of murine CD8+ T cells showed increased proliferative and cytolytic capacity in the absence of BACH2. Before activation, BACH2-deficient CD8+ T cells had a higher abundance of memory and reduced abundance of naïve cells compared to wild-type. CTLs derived from central memory T cells were more potently cytotoxic than those derived from naïve T cells, but even within separated subsets, BACH2-deficiency conferred a cytotoxic advantage. Immunofluorescence and electron microscopy revealed larger granules in BACH2-deficient compared to wild-type CTLs, and proteomic analysis showed an increase in granule content, including perforin and granzymes. Thus, the enhanced cytotoxicity observed in effector CTLs lacking BACH2 arises not only from differences in their initial differentiation state but also inherent production of enlarged cytolytic granules. These results demonstrate how a single gene deletion can produce a CTL super-killer.

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Bach2 keeps homeostasis in lung by regulating inflammatory response and maintaining function of alveolar macrophage.

Project description:Alveolar macrophages (AMs) of Bach2 KO mice show multiple alternations in their functions including lipid metabolism. We aimed to clarify the mechanism whereby deficiency of Bach2 impairs the function of AMs and ruins the homeostasis of lungs. Now we report that some cytokines produced from Bach2-deficient T cells alter the character of AMs and expression of Bach2 is necessary for AMs to maintain the function of lipid metabolism.

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Single cell gene expression profile of irradiated small intestinal crypt cells of WT and CREPT KO mice

Project description:To investigate the role of CREPT in intestinal regeneration, we performed single cell RNA sequencing (scRNA-seq) analyses on irradiated small intestinal crypt cells of WT and CREPT KO mice to figure out the change of different types of intestinal epithelial cells.

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Transcription profiling of jejunums from wild type and Klf9-/- mice to investigate the involvement of Klf9 in small intestine crypt-villus cell renewal and lineage determination.

Project description:Kruppel-like factor 9 (Klf9), a zinc-finger transcription factor, is implicated in the control of cell proliferation, cell differentiation and cell fate in brain and uterus. Using Klf9 null mutant mice, we have investigated the involvement of Klf9 in small intestine crypt-villus cell renewal and lineage determination. We report the predominant expression of Klf9 gene in small intestine smooth muscle (muscularis externa). Jejunums null for Klf9 have shorter villi, reduced crypt stem/transit cell proliferation, and altered lineage determination as indicated by decreased and increased numbers of Goblet and Paneth cells, respectively. A stimulatory role for Klf9 in villus cell migration was demonstrated by BrdU labeling. Results suggest that Klf9 controls the elaboration, from small intestine smooth muscle, of molecular mediator(s) of crypt cell proliferation and lineage determination, and of villus cell migration. Experiment Overall Design: Total RNA was extracted in parallel from the jejunums of five WT and five Klf9-/- male mice (PND 30) using TRIzol reagent (Invitrogen, Carlsbad, CA). Conversion of each RNA preparation to corresponding fragmented cRNA. Fifteen ug of each cRNA was hybridized for 16 hours to an Affymetrix mouse 430A GeneChip. Ten GeneChips (each corresponding to a single animal) were hybridized, washed and scanned in parallel. Following the wash, signal amplification, and signal detection steps, GeneChips were scanned (Agilent GeneArray laser scanner) and the resultant images quantified using Affymetrix MAS 5.0 software.

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Bach2 deficiency leads to spontaneous expansion of IL-4-producing T follicular helper cells and autoimmunity

Project description:The transcription factor Bach2 is a critical negative regulator of Tfh cell differentiation, especially IL-4 subset. Tfh cells from the mesenteric lymph nodes of WT and Bach2 CD4 conditional KO mice were collected to process the Rna-seq. Mechanistically, Bach2 may limit abnormal IL-4-produicng Tfh cell formation by repressing c-Maf, CXCR5 and IL-4.

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