RNA sequencing 10.5 dpc Rathke''s pouch with deletion of Shh
Ontology highlight
ABSTRACT:
INSTRUMENT(S): RNeasy Micro Kit (Qiagen), NextSeq 500
ORGANISM(S): Mus musculus
SUBMITTER: John Apps
PROVIDER: E-MTAB-5822 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:RNA sequencing 10.5 dpc Rathke's pouch with deletion of Shh
| PRJEB21321 | ENA
Project description:The most experiments about buccal pouch mucosal cells were investigated in mice and hamster. In these studies we have used porcine buccal pouch mucosal cells cultured primarily in vitro to investigate the expression profile of new molecular markers of mucosal wounding, vascularization and proliferation. In this study, we demonstrated the gene expression profile of long time primary cultured porcine buccal pouch mucosal cells.
2018-04-05 | GSE112659 | GEO
Project description:UC pouchitis is a potential model of UC. We prospectively examined the pouch transcriptomes of UC and familial adenomatous polyposis (FAP) IPAA patients to unveil molecular mechanisms of UC pouchitis susceptibility. Methods: Total RNA was isolated using the AllPrep DNA/RNA Mini Kit (QIAGEN, Cat No. 8020). RNA quality was evaluated using Bioanalyzer (Agilent, Santa Clara, CA). All RNA samples displayed RNA Integrity Number (RIN) >7. RNAseq including cDNA library preparation was processed at the Genomics Core Facility of University of Chicago (https://fgf.uchicago.edu/). Total RNA in the amount of 100-500μg per sample was depleted of ribosomal RNA using the Ribo-Zero kit (Epicentre, Madison, WI). The directional (first strand) cDNA libraries were prepared following the guide of TruSeq Stranded Total RNA Sample Preparation kit. Results: Unlike FAP patients, UC subjects exhibited a large set of differentially expressed genes (DEGs) between pouch and pre-pouch mucosa as early as 4 months after pouch functionalization. Functional pathway analysis of DEGs in UC pouch revealed: (1) Gain of colon-associated gene expressions and loss of ileum associated gene expressions, (2) enhanced state of immune/inflammatory response, and (3) suppressed xenobiotic, lipid, and bile acid metabolic pathways. These changes were corroborated upon reanalysis of a published larger cross-sectional study of UC and FAP patients. Moreover, >70% of DEGs mapped to published IBD and normal colonic microarray datasets displayed directional changes consistent with active UC, but not Crohn's disease. Conclusions: UC patients exhibit a unique transcriptomic response to ileal pouch creation that can be observed well before disease. The transcriptome alterations provide insights into pouchitis
2016-05-11 | GSE81266 | GEO
Project description:Restorative proctocolectomy with ileal pouch-anal anastomosis is a surgical procedure in patients with ulcerative colitis refractory to medical therapies. Pouchitis, the most common complication, is inflammation of the pouch of unknown etiology. To define how the intestinal immune system is distinctly organized in response to inflammation and to develop mechanistic hypotheses of pouchitis, we analyzed tissues from patients with and without pouchitis and from patients with ulcerative colitis using single-cell RNA sequencing. We examined pouch lamina propria CD45+ hematopoietic cells from intestinal tissues of ulcerative colitis patients with (n=15) and without an ileal pouch-anal anastomosis (n=11). Further in silico meta-analysis was performed to generate transcriptional interaction networks and identify drug targets for patients with inflamed pouches. We identified a population of IL1B+ antimicrobial macrophages and FOXP3+/BATF+ T cells that are expanded in inflamed tissues, which we further validated in other single cell RNA-seq datasets from IBD patients. Cell type specific markers obtained from single-cell RNA-sequencing was used to infer representation from bulk RNA sequencing datasets, which further implicated antimicrobial macrophages expressing IL1B with S100A8/A9 calprotectin as being associated with inflammation, and Bacteroidiales and Clostridiales bacterial taxa. We found that non-responsiveness to anti-integrin biologic therapies in ulcerative colitis patients was associated with the signature of this antimicrobial macrophage population in a subset of patients. This study identified conserved and distinct features of intestinal inflammation between parts of the small and large intestine undergoing similar inflammation conditions. Specifically, we relate inflammation of the pouch, a surgically constructed organ, to other inflammatory contexts throughout the gastrointestinal tract.
2020-12-01 | GSE162335 | GEO
Project description:The pathophysiology of Crohn’s-like disease of the pouch (CDP) that develops after restorative proctocolectomy with ileal pouch-anal anastomosis (IPAA) for ulcerative colitis (UC) is unknown. We examined mucosal cells from patients with and without CDP using single cell analyses.
2024-08-02 | GSE246987 | GEO
Project description:<p>This study involved evaluation of the tissue associated microbiome of the ileal pouch following surgery for ulcerative colitis (UC) or familial adenomatous polyposis (FAP). Individuals were recruited, with biopsies taken from the ileal pouch and the pre-pouch ileum, microbial DNA was extracted and sequenced using 454 pyrosequencing. Total bacterial community structure and abundance were evaluated to determine which changes were characteristic of inflammatory phenotypes including pouchitis (inflammation of the ileal pouch) and a Crohn's disease-like phenotype.</p>
| phs000659.v1.p1 | EGA
Project description:To examine the mechanism underlying chemoprevention and changes in gene expression pattern induced by chlorophyllin and ellagic acid during 7,12-dimethylbenz[a]anthracene (DMBA)-induced hamster buccal pouch (HBP) carcinogenesis
2011-06-02 | GSE29679 | GEO
Project description:Mast cells (MCs) were implicated in tissue remodelling in hamster models of heart inflammatory diseases. Here we asked whether MCs promote inflammatory neovascularization in hamster cheek pouch (HCP) parasitized by Trypanosoma cruzi, the protozoan that causes Chagas disease. Intravital microscopy (IVM) performed 3 days after inoculation of Dm28c trypomastigote (GFP-TCTs) showed a subtle infiltration of rhodamine-labeled leukocytes. Interestingly, the baseline levels of FITC-dextran leakage (3 dpi) were consistently increased, raising the possibility that intracellular amastigotes may coopt the low-grade inflammation to facilitate the delivery of plasma-borne nutrients during the period in which host cells must metabolically sustain parasite division. Although proangiogenic indexes were only mildly stimulated at 3 dpi, we found a positive correlation with transcription of proinflammatory cytokines (pro-IL- and IFN-). Having established 3 dpi as a timepoint in which vascular remodeling was already measurable, we next compared the proteomic profiles of parasitized HCP with those of internal controls (PBS injected 3 days earlier in the contralateral pouch) we found 87 proteins upregulated, and 17 were downregulated in the parasitized HCP. Minor changes in protein expression were observed in response to PBS injection (2 upregulated and 12 downregulated proteins. Congruent with the increased density of MCs observed in parasitized HCP (histological analysis), the MC protease 1 (chymase) stood out as the most abundant sequence. Interestingly, toluidine blue staining appointed clusters of MCs degranulating at 3 dpi. Noteworthy, two plasma proteins (complement C3 and serum albumin) were also identified as major proteins, further suggesting that leaky capillaries irrigated the HCP at early stages (3 dpi) of infection . Detection of cytokines or classical proangiogenic factors was beyond the sensitivity of our methods.
2022-04-04 | PXD026905 | Pride
Project description:A total proctocolectomy with ileal pouch-anal anastomosis (IPAA) is considered the surgery of choice for definitive management of familial adenomatous polyposis (FAP) and selected patients with ulcerative colitis (UC). However, this surgical treatment often associates with a long-term complication, pouchitis, which occurs mostly in UC patients. To better define the molecular background of pouchitis, the microarray-based survey was performed using pouch mucosal samples collected from 28 and 8 patients operated for UC and FAP, respectively. A number of 4771 genes was significantly differentiating uninflamed from inflamed mucosal samples, and their functional features were represented mostly by alerted metabolic and cell proliferation pathways. In contrast, functional analyses of aberrantly expressed probe sets between UC and FAP samples, irrespectively of mucosal inflammation status, revealed multiple pathways and terms which were linked to changes in immune response. Noteworthy, the comparison of uninflamed UC and FAP samples distinguished a set of 26 altered mRNAs including inflammation-related transcript encoding a Charcot-Leyden crystal (CLC) protein. The most discrete changes in gene expression profiles differentiating uninflamed UC and FAP mucosal samples were attributed to a Gene Ontology category innate immune response. Our study confirmed alterations of the immune responses as dominant in UC pouchitis which were earlier found in the studies using analyses of singular molecular elements. This observation may be important when managing IPAA patients. Each sample represents three biopsies taken from single patient, from the same areas of the lower part of the pouch mucosa (above the rectal cuff) during endoscopic examination. 28 patients underwent surgery for UC and 8 patients for FAP.
2014-05-01 | E-GEOD-50788 | biostudies-arrayexpress
Project description:Objective. To identify novel monosodium urate (MSU) crystal-induced mRNAs by transcript profiling of isolated murine air pouch membranes. Methods. Nine hours after injecting crystals into air pouches, membranes were meticulously dissected away from the adjacent soft tissues. mRNA expression differences between inflamed and control membranes were determined by oligonucleotide microarray analysis. Induction of selected mRNAs was validated by real-time relative quantitative reverse transcriptase PCR (qPCR) in pouch membranes and murine peritoneal macrophages. Results. Eleven of the 12 most highly upregulated mRNAs related to innate immunity and inflammation. They included mRNAs encoding histidine decarboxylase (the enzyme that synthesizes histamine), interleukin (IL)-6, the cell surface receptors PUMA-g and TREM-1, and the polypeptides Irg1 and PROK-2. MSU crystals induced dramatic rises in these mRNAs in the pouch membrane within 3-8 hours after the surge in pro-inflammatory cytokine (IL-6, IL-1beta and TNFalpha) and immediate early gene (Egr-1) transcription, which occurred 1h after crystal injection. MSU crystals induced these mRNAs in cultured macrophages with similar kinetics but lower fold changes. In keeping with their downregulation by MSU crystals according to the microarrays, qPCR confirmed that TREM-2 and granzyme D mRNAs decreased 79% and 94%, respectively, in MSU crystal inflamed membranes. Conclusions. This analysis disclosed several genes previously not implicated in MSU crystal inflammation. Their rise after the early surge in cytokine mRNAs suggests that they may, for instance, amplify or perpetuate inflammation. Transcript profiling of the isolated air pouch membrane promises to be a powerful tool to identify genes acting at different stages of inflammation. Experiment Overall Design: Mouse strain: female Balb/C, 6-8 weeks old Experiment Overall Design: Number of mice= 6. Experiment Overall Design: Air pouches raised on back for 7 days by injecting 2ml of sterile air. Experiment Overall Design: On day 7, injection of 1ml PBS or 2mg MSU crystals in 1ml PBS (n=3 each) Experiment Overall Design: 9 h after injection, dissection of the air pouch membranes from the adjacent soft tissues, RNA extraction with RNeasy columns. Pooling of RNA from the 3 control pouches or the 3 MSU crystal pouches. Processing and labeling of 5ug aliquots in the U Penn microarray core according to standard Affy protocols. Hybridization to Affy Mo430_2 oligonucleotide microarrays.
2008-06-18 | E-GEOD-11498 | biostudies-arrayexpress