Dissection of gastric homeostasis in vivo facilitates permanent capture of isthmus stem cells in vitro [single-cell RNA-seq]
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ABSTRACT:
PROVIDER: PRJNA899079 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22220900_1.fastq.gz | Fastqsanger.gz | |||
| SRR22220900_2.fastq.gz | Fastqsanger.gz | |||
| SRR22220901_1.fastq.gz | Fastqsanger.gz | |||
| SRR22220901_2.fastq.gz | Fastqsanger.gz | |||
| SRR22220902_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:The glandular stomach is comprised of two anatomically and functionally distinct epithelial tissues termed corpus and antrum. While these compartments continuously regenerate to ensure normal organ function, our understanding of the molecular and cellular determinants that maintain these tissues remains incomplete. Here, we established an unbiased account of all gastric epithelial cells of the mouse corpus and antrum using single cell RNA-sequencing, allowing us to compare these adjacent epithelia and their stem cell compartments. Our data reveals that epithelial cell types with equivalent functional roles in the corpus and antrum utilize similar transcriptional programs, and our results support the existence of two discernible stem cell populations within the gland base and isthmus regions of these tissues. To study isthmus stem cells, typically underrepresented in conventional, gland base-enriched organoid cultures, we developed a novel 2D monolayer culture system to propagate mouse and human gastric epithelia. These 2D cultures expand indefinitely via Lgr5- isthmus-like cells and maintain the ability to differentiate into diverse gastric cell types. While 2D corpus and antrum cultures were transcriptionally similar, they retained a molecular memory and differentiation bias that mirrored their tissue of origin. Furthermore, gastric 2D cultures could be readily and reversibly converted into conventional 3D organoids, highlighting the remarkable plasticity of undifferentiated stomach epithelial cells. Finally, we utilized the 2D culture system to show that rare primary epithelial cells with high levels of Sox2 expression, previously hypothesized to be gastric stem cells, most closely resembled enterochromaffin (EC) cells and Sox2 is both necessary and sufficient to generate EC cells in vivo. Together, our data (i) provide important insights into the basis of gastric epithelial regeneration and differentiation, (ii) establish a tractable 2D culture system to capture and manipulate primary gastric isthmus stem cells in vitro and (iii) uncover a role for the stem cell factor Sox2 during EC cell specification.
2022-11-10 | GSE217472 | GEO
Project description:The glandular stomach is comprised of two regenerative compartments termed corpus and antrum, yet our understanding of the cell populations that maintain these epithelia is incomplete. Here, we show that cell types with equivalent functional roles in the corpus and antrum share similar transcriptional states including the immature isthmus population. To study isthmus cells, we developed a monolayer (2D) culture that is continually maintained via Lgr5-negative cells and produces diverse gastric cell types. Importantly, 2D cultures can be interconverted into conventional 3D organoids, recapitulating the plasticity of gastric epithelial cells in vivo. Finally, we utilized the 2D culture system to show that rare Sox2-expressing cells resemble enterochromaffin (EC) cells and Sox2 is both necessary and sufficient to generate EC cells. Together, our data provide important insights into the basis of gastric homeostasis, establish a tractable culture system to capture isthmus cells and uncover a role for Sox2 in EC cells.
2022-11-10 | GSE217471 | GEO
Project description:The glandular stomach is comprised of two regenerative compartments termed corpus and antrum, yet our understanding of the cell populations that maintain these epithelia is incomplete. Here, we show that cell types with equivalent functional roles in the corpus and antrum share similar transcriptional states including the immature isthmus population. To study isthmus cells, we developed a monolayer (2D) culture that is continually maintained via Lgr5-negative cells and produces diverse gastric cell types. Importantly, 2D cultures can be interconverted into conventional 3D organoids, recapitulating the plasticity of gastric epithelial cells in vivo. Finally, we utilized the 2D culture system to show that rare Sox2-expressing cells resemble enterochromaffin (EC) cells and Sox2 is both necessary and sufficient to generate EC cells. Together, our data provide important insights into the basis of gastric homeostasis, establish a tractable culture system to capture isthmus cells and uncover a role for Sox2 in EC cells.
2022-11-10 | GSE217470 | GEO
Project description:Dissection of gastric homeostasis in vivo facilitates permenant capture of isthmus stem cells in vitro
| PRJNA899074 | ENA
Project description:Dissection of gastric homeostasis in vivo facilitates permenant capture of isthmus stem cells in vitro [Lgr5, Sox2]
| PRJNA899077 | ENA
Project description:Dissection of gastric homeostasis in vivo facilitates permenant capture of isthmus stem cells in vitro [2D culture]
| PRJNA899078 | ENA
Project description:This SuperSeries is composed of the SubSeries listed below.
2022-11-10 | GSE217473 | GEO
Project description:The Del-Mar 14K chip was used to interrogate differential expression of transcripts in the white isthmus (WI) compared with the adjacent magnum (Mg) and uterine (Ut) segments of the hen oviduct. Differential expression of genes common to both comparisons (WI/Mg and WI/Ut) was detected for 204 annotated proteins. Of these, 58 genes were overexpressed in both WI/Mg and WI/Ut, and are therefore considered to be the most interesting candidates for WI - specific functions. Additionally, general analysis revealed 135 clones hybridizing to overexpressed transcripts (WI/Mg + WI/Ut), and corresponding to 102 NCBI annotatated non-redundant Gallus gallus gene ID~s. This combined analysis revealed that structural proteins highly over-expressed in white isthmus were collagen X (COL10A1), Fibrillin (FBN1) and Cysteine Rich Eggshell Membrane Protein (CREMP). In addition, genes encoding collagen-processing enzymes were over-expressed, as were proteins known to regulate disulfide cross-linking, suggesting that coordinated upregulation of gene networks in the white isthmus is associated with eggshell membrane fibre formation. IPA interactome analysis reinforces the key role of the estrogen receptor and SMAD3 in mediating gene regulation during eggshell membrane synthesis. These results will assist with development of selection strategies to improve eggshell quality and food safety of the table egg. Keywords: Laying hen, eggshell, oviduct, Isthmus expression, cDNA microarray, indirect cDNA labelling, Alexa Fluor dyes Keywords: Expression profiling by array A balanced block hybridization design (Dye switch) was used where half of the samples were labelled with AlexaM-BM-. 555 fluorescent dye and the other half with AlexaM-BM-. 647. A total of 16 microarray slides were used for hybridization to 32 samples that correspond to four tissue contrast (White isthmus versus magnum and uterus versus white isthmus).
2013-12-01 | E-GEOD-52491 | biostudies-arrayexpress
Project description:The Del-Mar 14K chip was used to interrogate differential expression of transcripts in the white isthmus (WI) compared with the adjacent magnum (Mg) and uterine (Ut) segments of the hen oviduct. Differential expression of genes common to both comparisons (WI/Mg and WI/Ut) was detected for 204 annotated proteins. Of these, 58 genes were overexpressed in both WI/Mg and WI/Ut, and are therefore considered to be the most interesting candidates for WI - specific functions. Additionally, general analysis revealed 135 clones hybridizing to overexpressed transcripts (WI/Mg + WI/Ut), and corresponding to 102 NCBI annotatated non-redundant Gallus gallus gene ID~s. This combined analysis revealed that structural proteins highly over-expressed in white isthmus were collagen X (COL10A1), Fibrillin (FBN1) and Cysteine Rich Eggshell Membrane Protein (CREMP). In addition, genes encoding collagen-processing enzymes were over-expressed, as were proteins known to regulate disulfide cross-linking, suggesting that coordinated upregulation of gene networks in the white isthmus is associated with eggshell membrane fibre formation. IPA interactome analysis reinforces the key role of the estrogen receptor and SMAD3 in mediating gene regulation during eggshell membrane synthesis. These results will assist with development of selection strategies to improve eggshell quality and food safety of the table egg. Keywords: Laying hen, eggshell, oviduct, Isthmus expression, cDNA microarray, indirect cDNA labelling, Alexa Fluor dyes Keywords: Expression profiling by array
2013-12-01 | GSE52491 | GEO
Project description:Purpose: evaluate if different proestrus-estrus concentrations of estradiol (E2) and metestrus progesterone (P4) concentrations specifically regulate oviductal gene expression. Methods: ampulla and isthmus samples of animals whit a large pre-ovulatory follicle and a large CL (LF/LCL) and animals whit a small pre-ovulatory follicle and a small CL (SF/SCL) were collected after slaughter at day four of the estrous cycle. Total RNA was extracted and RNA sequencing was performed using the Illumina HiScanSeq (ampulla samples) and the Illumina HiSeq 2500 (isthmus samples) platforms. Results: After using HTSeq-count, approximately ~60% of the total reads uniquely mapped to the UMD 3.1 reference genome. In the ampulla samples, a total of 692 genes showed differential expression, of which 325 and 367 were up-regulated in the LF-LCL and SF-SCL samples, respectively. In the isthmus samples, a total of 590 genes showed differential expression, of which 274 and 316 were up-regulated in the isthmus of LF/LCL and SF/SCL samples, respectively. Conclusions: Our study represents the first detailed analysis of oviduct transcriptomes, generated by RNA-seq technology. Differential global gene expression profiles identified indicate that the biology of the bovine oviductal tissue is modulated by the periovulatory endocrine milieu. The LF-LCL group transcriptome may potentially reveal molecules associated with higher fertility. Oviductal mRNA profiles of cows whit different endocrine milleus were generated by next generation sequencing.
2016-06-30 | E-GEOD-65680 | biostudies-arrayexpress