Mardiyyah/TAPT_data_V2_split · Datasets at Hugging Face

PMCID stringclasses 24 values	Title stringclasses 24 values	Sentences stringlengths 2 40.7k
PMC12133578	Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.	A PhiX library spike-in was added (10%) due to the low diversity of the TCR library, before 300-bp paired-end sequencing on an Illumina MiSeq instrument at the Oxford Genomics Centre.
PMC12133578	Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.	This was an observational, descriptive study.
PMC12133578	Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.	The experiments were not randomized.
PMC12133578	Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.	No statistical method was used to predetermine sample size, but our sample sizes are similar to those reported in previous publications.
PMC12133578	Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.	No data were excluded from analyses.
PMC12133578	Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.	The investigators were not blinded to allocation during experiments and outcome assessment.
PMC12133578	Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.	Data collection and analysis were not performed blind to the conditions of the experiments.
PMC12133578	Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.	Data distributions of transcriptomics datasets were tested to ensure they met the assumptions of statistical tests.
PMC12133578	Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.	For other datasets, data distribution was assumed to be normal, but this was not formally tested.
PMC12133578	Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.	All statistical analyses and graphs, except transcriptional data, were performed using Prism Software v9 and v10 (GraphPad).
PMC12133578	Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.	Specific statistical tests are described in relevant figure legends.
PMC12133578	Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.	All data are presented as the mean ± s.e.m.
PMC12133578	Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.	unless stated otherwise.
PMC12133578	Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.	Flow cytometry data were analyzed using FlowJo v9.9.5 and v10.6.1.
PMC12133578	Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.	Raw sequencing read data were subjected to quality control and aligned to the human reference hg38 genome using STAR aligner.
PMC12133578	Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.	The DESeq2 R package was used for downstream differential expression analysis.
PMC12133578	Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.	Bulk TCR repertoire analysis was performed using the iRepertoire analysis pipeline.
PMC12133578	Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.	Raw read data were processed with either the Cell Ranger pipeline or the BD Genomics pipeline.
PMC12133578	Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.	Downstream analyses were carried out in R using the Seurat pipeline.
PMC12133578	Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.	Raw read data were processed using the Space Ranger pipeline.
PMC12133578	Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.	Downstream analyses were carried out in R using the Seurat pipeline.
PMC12133578	Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.	Raw sequencing read data were processed with the Cell Ranger VDJ pipeline.
PMC12133578	Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.	Downstream analyses were carried out in R. Additional details for computational data analysis are provided in Supplementary Methods.
PMC12133578	Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.	Further information on research design is available in the Nature Portfolio Reporting Summary linked to this article.
PMC12133578	Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.	Any methods, additional references, Nature Portfolio reporting summaries, source data, extended data, supplementary information, acknowledgements, peer review information; details of author contributions and competing interests; and statements of data and code availability are available at 10.1038/s41590-025-02146-2.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	Using antibodies to specific protein antigens is the method of choice to assign and identify cell lineage through simultaneous analysis of surface molecules and intracellular markers.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	Embryonic stem cell research can be benefited from using antibodies specific to transcriptional factors/markers that contribute to the "stemness" phenotype or critical for cell lineage.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	In this report, we have developed and validated antibodies (either monoclonal or polyclonal) specific to human embryonic stem cell antigens and early differentiation transcriptional factors/markers that are critical for cell differentiation into definite lineage.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	These antibodies enable stem cell biologists to conveniently identify stem cell characteristics and to quantitatively assess differentiation.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	Although the stem cell concept was introduced decades ago, to date, stem cells can only be defined functionally, not morphologically or phenotypically.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	Two functions define stem cells.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	Firstly, they are self-renewing, thus able to propagate to generate additional stem cells.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	Secondly they can differentiate into various progenitor cells, which commit to further maturation along a specific lineage.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	While stem cells can be best defined functionally, a good number of molecular markers have been used to prospectively identify various stem cell populations.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	Although the functional importance of many of these antigens remains unknown, their unique expression pattern and timing of expression provide a useful tool for scientists to identify as well as isolate stem cells.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	Embryonic stem cells (ESC), derived from the inner cell mass of pre-implantation embryos, have been recognized as the earliest stem cell population .
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	This pluripotent population can differentiate into all somatic tissue including germ cells.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	In the case of human ESC, they can differentiate into some extra-embryonic derivatives as well.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	Like mouse ESC, human ES cells can be maintained and propagated on mouse fibroblast feeders for extended periods in media containing basic fibroblast growth factor (bFGF) .
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	Gene expression of undifferentiated human ES cells has been investigated among several ES cell lines by a variety of techniques.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	They include comparison with databases, reverse transcriptase-polymerase chain reaction, focused cDNA microarrays, and immunocytochemistry.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	A list of molecules comprised of known ES-specific or -highly expressed genes and candidates that can serve as markers for human ESCs and may also contribute to the "stemness" phenotype has been established [3-11].
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	For example, pluripotent ESC can be characterized by high level expression of Oct3/4 (POU domain, class 5, transcription factor 1, Pou5f1) and Nanog, which are a member of POU domain and homeobox transcription factors respectively.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	A critical amount of Oct3/4 and Nanog expression is required to sustain stem-cell pluripotency and both of these markers are downregulated as cells differentiate in vitro and in vivo [4-9].
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	Antibodies to Oct3/4 which cross react with human Oct 3/4 have been widely used to monitor the presence of undifferentiated ESC.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	No single marker however is sufficient or unique for identifying ESCs.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	Oct3/4 for example is expressed by germ cells and may be expressed by specific populations later in development.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	Likewise, Nanog has been shown to express in other tissues.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	We and other have noted however, that while no single marker is sufficient a constellation of positive and negative markers can in concert unambiguously allow one to define the state of ESC cultures and that surface markers in combination can be used to prospectively sort for ESC.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	Based on published data at the level of gene expression, we have cloned a number of candidate marker genes.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	We have also expressed the recombinant protein and generated a panel of monoclonal or polyclonal antibodies to these proteins.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	Using these antibodies we have confirmed the specificity and selectivity of these antibodies on several ESC lines and established their utility as stem cells markers.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	Our results confirm the expression pattern and timing of these cell markers at the protein level, whereas previous data reported at the level of gene expression.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	All monoclonal antibodies were initially selected for their abilities to recognize recombinant proteins in direct ELISAs.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	A subset were also tested by Western Blot analysis using recombinant proteins and cell lysate to confirm binding to a single epitope.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	The best clone was later screened for its applications for immunocytochemistry and flow cytometry using various cell lines.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	Human peripheral blood platelets were used for screening mouse anti-human CD9 antibody.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	MCF-7 cells were used for screening mouse anti-human E-Cadherin and PODXL (podocalyxin-like) antibodies.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	MG-63 cells were used for screening mouse anti-human GATA1 (GATA binding protein 1) antibody.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	Beta-TC6 cells were used for screening for mouse anti-human/mouse PDX-1 (pancreatic duodenal homeobox-1) antibody.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	NTERA-2 cells were used for screening mouse anti-human Oct3/4 and SOX2 (sex-determining region Y-box 2) antibodies.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	All polyclonal antibodies were affinity-purified using recombinant proteins and validated by direct ELISAs and Western.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	Caco-2 cells were used for validation of goat anti-human GATA6 antibody and NTERA-2 cells were used for validation of goat anti-human Nanog and anti-human Oct3/4 antibodies (Summarized in Table 1).
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	Summary list of antibody verification by western blot.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	N/A: 1.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	DPPA5 is still being subcloned.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	Only Elisa verification is available.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	2.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	The clone for GATA-1 (MAB1779) does not work for Western blot application but is useful for IHC, The clone picked for Western blot analysis does not work for IHC (MAB17791, see data in ).
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	After antibodies were validated in direct ELISAs, Western blot or cell lines (Fig. 1 and data not shown), they were used to examine the expression of individual molecules in undifferentiated human ES cells and differentiated EBs.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	When examined by immunohistochemistry, high level of expressions of Oct3/4, SOX2, E-Cadherin, PODXL and Nanog were observed in undifferentiated human ES cells (Fig. 2A, 2B and 2C).
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	DPPA5 (developmental pluripotency associated 5) expression was also observed in undifferentiated human ES cells (data not shown).
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	We noted that a subset of the proteins used were membrane bound proteins.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	To test if any of the antibodies generated could recognize an extracellular epitope and thus be used for live cell sorting, we repeated staining of live cells as previously described.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	The CD9, E-Cadherin and PODXL antibodies recognized an extracellular epitope and their ability to select cells by FACS was confirmed (Fig. 3).
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	Minimal or no expressions of Oct3/4, E-Cadherin, PODXL and Nanog were detected in the differentiated EBs (Fig. 2D, 2E and 2F).
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	However, SOX2 expression, which is observed in neural progenitor cells, is persistent in subsets of EBs.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	Western blot analysis for Gt × hOct3/4 (A), Gt × hNanog (B) and Ms × hSOX2 (C) in NTERA-2 cell lysate, Ms × hE-Cadherin (D) in MCF-7 cell lysate, Ms × hCD9 (E) in PBMC lysate and Ms × hPDX-1(F) in β-TC-6 cell lysate.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	Numbers indicate the positions of molecular weight markers.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	Undifferentiated human ES cells (A, B, and C) and differentiated EBs (D, E and F) were analyzed using antibodies to indicated molecular markers.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	Immunostaining with goat anti-human Oct3/4 (Red in A and D), mouse anti-human SOX2 (Green in A and D), goat anti-human E-Cadherin (Red in B and E), mouse anti-human PODXL (Green in B and E), and goat anti-human Nanog (Red in C and F), are contrasted with DAPI nuclear staining (Blue in C-F).
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	Note the dramatic downregulation of ESC specific markers (Oct3/4, E-Cadherin, PODXL, and Nanog) in EBs.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	However, SOX2 expression is persistent in subsets of EB cells.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	Scale bars = 100 μm.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	Human embryonic stem cells stained with anti-CD9 (A), anti-E-Cadherin (B), and anti-PODXL (C) and antigen expression detected by a flow cytometer.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	The specific staining is indicated by green histogram and corresponding isotype control is indicated by black histogram.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	Suspension culture with FGF withdrawal is known to induce differentiation of ES cells to all three germ layer precursors .
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	The differentiation status of the EB used here was detected to contain all germ cell markers by RT-PCR (Fig. 4).
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	In order to examine how more antibodies can be used for characterization of early differentiation events from human ES cells, we examined the expressions of endodermal markers, SOX17, GATA6 and PDX-1, and mesodermal markers, Brachyury and GATA1, in the undifferentiated human ES cells and differentiated EBs.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	Expressions of SOX17, GATA6, PDX-1, Brachyury and GATA1 were not detected in undifferentiated human ES cells (data not shown).
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	In contrast to the undifferentiated ES cells, subpopulations of SOX17-, GATA6-, Brachyury- and GATA1-positive cells were observed (Fig 4).
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	These results suggest that both endodermal and mesodermal precursors exist in EBs with FGF withdrawal for 8 days.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	However, no PDX-1-positive cells were seen in EBs differentiated with the same treatment (data not shown).
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	Differentiated EBs were analyzed by either immunocytochemistry or RT-PCR to the indicated molecular markers. (
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	A) Immunostaining with goat anti-human SOX17 (Red), is contrasted with Fluoro Nissl nuclear staining (Green). (
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	B) Immunostaining with goat anti-human GATA6 (Red), is contrasted with DAPI nuclear staining (Blue). (
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	C) Immunostaining with goat anti-human brachyury (Red), is contrasted with DAPI nuclear staining (Blue). (
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	D) Immunostaining with mouse anti-human GATA1 (Red).
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	Note that each antibody recognizes subsets of EB cells.
PMC1315352	Development of antibodies to human embryonic stem cell antigens.	Scale bars = 100 μm. (

PMC12133578

Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.

A PhiX library spike-in was added (10%) due to the low diversity of the TCR library, before 300-bp paired-end sequencing on an Illumina MiSeq instrument at the Oxford Genomics Centre.

PMC12133578

Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.

This was an observational, descriptive study.

PMC12133578

Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.

The experiments were not randomized.

PMC12133578

Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.

No statistical method was used to predetermine sample size, but our sample sizes are similar to those reported in previous publications.

PMC12133578

Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.

No data were excluded from analyses.

PMC12133578

Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.

The investigators were not blinded to allocation during experiments and outcome assessment.

PMC12133578

Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.

Data collection and analysis were not performed blind to the conditions of the experiments.

PMC12133578

Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.

Data distributions of transcriptomics datasets were tested to ensure they met the assumptions of statistical tests.

PMC12133578

Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.

For other datasets, data distribution was assumed to be normal, but this was not formally tested.

PMC12133578

Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.

All statistical analyses and graphs, except transcriptional data, were performed using Prism Software v9 and v10 (GraphPad).

PMC12133578

Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.

Specific statistical tests are described in relevant figure legends.

PMC12133578

Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.

All data are presented as the mean ± s.e.m.

PMC12133578

Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.

unless stated otherwise.

PMC12133578

Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.

Flow cytometry data were analyzed using FlowJo v9.9.5 and v10.6.1.

PMC12133578

Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.

Raw sequencing read data were subjected to quality control and aligned to the human reference hg38 genome using STAR aligner.

PMC12133578

Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.

The DESeq2 R package was used for downstream differential expression analysis.

PMC12133578

Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.

Bulk TCR repertoire analysis was performed using the iRepertoire analysis pipeline.

PMC12133578

Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.

Raw read data were processed with either the Cell Ranger pipeline or the BD Genomics pipeline.

PMC12133578

Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.

Downstream analyses were carried out in R using the Seurat pipeline.

PMC12133578

Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.

Raw read data were processed using the Space Ranger pipeline.

PMC12133578

Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.

Downstream analyses were carried out in R using the Seurat pipeline.

PMC12133578

Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.

Raw sequencing read data were processed with the Cell Ranger VDJ pipeline.

PMC12133578

Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.

Downstream analyses were carried out in R. Additional details for computational data analysis are provided in Supplementary Methods.

PMC12133578

Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.

Further information on research design is available in the Nature Portfolio Reporting Summary linked to this article.

PMC12133578

Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.

Any methods, additional references, Nature Portfolio reporting summaries, source data, extended data, supplementary information, acknowledgements, peer review information; details of author contributions and competing interests; and statements of data and code availability are available at 10.1038/s41590-025-02146-2.

PMC1315352