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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression data of freshly microdissected human hair follicle dermal papilla and its comparisons

ABSTRACT: The dermal papilla (DP) of the hair follicle plays crucial roles in the hair follcie morphogenesis and cycling. Thus, the elucication of human DP molecular signature is of great interest. DP cell culture by conventional method impairs intrinsic properties of DP cells. Isolatoion of human DP is hampered by the lack of specific cell surface markers. Thus, it still depends on manual microdissection, with which the removal of minor contamination is unfeasible. Cultured DP cells are mostly pure. Aggregation of cultured DP cells was shown to restore some intrinsic properties in cultured DP cells. Fibroblasts are distinct dermal cell population and provide baseline for DP arrays. Four sets of Genechip microarrays were generated from freshly-microdissected DPs (fDP), cultured DP cells (cDP), cultured fibroblasts (Fibro) collected from respective volunteers. Two sets of Genechips were additionally prepared from aggregated DP cells (agDP) and cultured DP cells which were used for the generation of agDPs (each set derived from respective volunteer). These Genechips can be compared to elucidate the genes possibly contribute to intrinsic property of intact human DPs. For instance, comparisons between cultured DP (cDP) and fibroblast (Fibro) or between aggregated DP (agDP) and cDP could sort out potential DP signature genes, as each population is predominantly consisted of DP cells. When the expression levels of those genes were compared between fDP and cDP chips, the genes up- or equally expressed in fDPs should represent DP signature genes.

ORGANISM(S): Homo sapiens

SUBMITTER: Manabu Ohyama

PROVIDER: E-GEOD-31324 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression data of freshly microdissected human hair follicle dermal papilla and its comparisons

Project description:The dermal papilla (DP) of the hair follicle plays crucial roles in the hair follcie morphogenesis and cycling. Thus, the elucication of human DP molecular signature is of great interest. DP cell culture by conventional method impairs intrinsic properties of DP cells. Isolatoion of human DP is hampered by the lack of specific cell surface markers. Thus, it still depends on manual microdissection, with which the removal of minor contamination is unfeasible. Cultured DP cells are mostly pure. Aggregation of cultured DP cells was shown to restore some intrinsic properties in cultured DP cells. Fibroblasts are distinct dermal cell population and provide baseline for DP arrays.

2011-08-11 | GSE31324 | GEO

Identification of therapeutic targets for glioblastoma by network analysis

Project description:In this study, we confirmed that transformed dedifferentiated astrocytes and neurons acquired a stem/progenitor cell state, although they still retained gene expression memory from their parental cell-type. Transcriptional network analysis on transformed cells revealed up-regulation of genes involved in three signaling pathways: Wnt signaling, cell cycle and focal adhesion with the gene Spp1, also known as osteopontin (OPN) serving as a key node connecting these three pathways. Inhibition of OPN blocked the formation of aggregated neurospheres, affected the proliferative capacity of transformed cell-types and reduced the expression levels of neural stem cell markers. Specific inhibition of OPN in murine glioma tumors prolonged mice survival. We conclude that OPN is an important player in dedifferentiation of cells during tumor formation, hence its inhibition can be a therapeutic target for glioblastoma. Cortical neurons and astrocytes were derived from 11 days old SynapsinI-Cre and GFAP-Cre mice, respectively. The cells were cultured in their respective media to maintain their identity. These cells were then transduced with HRas-shp53 lentivirus with a transduction efficiency of >90%. The transduced neurons and astrocytes were later switched to neural stem cell media devoid of serum and supplemented with FGF-2 (NSC media). Within one week, these cells became proliferative and aggregated to form free-floating neurospheres. These cells, hereinafter referred to as NSynR53 and AGR53, respectively, were later harvested and mRNA collected for sequencing library generation using DP-seq. To assess the regression of these cells to an undifferentiated state along the differentiation axis, enriched populations of mESC and NSC were also grown in vitro and mRNA obtained from these cells were subjected to sequencing library preparation.

2015-05-11 | E-GEOD-64411 | biostudies-arrayexpress

RNAseq changes in fibroblasts after treatment with selected protein(s) or E16.5 skin extract

Project description:Purpose: To identify the cellular processes upregulated in fibroblasts after treatment with selected protein(s) or E16.5 skin extract Methods: To explore the mechanism of extract-induced HF neogenesis, adult dermal fibroblasts were cultured in the presence of E16.5 extract or selected protein(s) for 3 days before being tested. Results: we determined how the exposure of adult fibroblasts to E16.5 extract, the selected protein mix or each of the selected proteins and compared the resultant transcriptomes with those of adult DP and embryonic dermal fibroblasts. Conclusions: Gene expression of adult fibroblasts exposed to E16.5 extract and selected proteins mix, the key DP signature genes became upregulated. Fibroblasts mRNA profiles of mouse with different treatments and adult DP and embryonic dermal fibroblasts were generated by next generation sequencing. SRA study accession: SRP081009; BioProject accession: PRJNA337890

2016-08-10 | E-GEOD-85303 | biostudies-arrayexpress

Low-input bulk RNA sequencing of thymic, mediastinal adipose tissue, and aortic arch CD4+CD8+ (DP) cells

Project description:Purpose: To establish if and how mediastinal and adipose tissue and aortic arch CD4+CD8+TCRb- cells (DPs) would differ from thymic DPs, we sorted DPs from all three regions by flow cytometry and subjected the cells to a low-input deep transcriptional profiling assay. Methods: Thymi, mediastinal adipose tissue, and aortic arches of five female, 8-week-old C57BL/6J mice were collected and pooled. Aortic arches and mediastinal adipose tissue were digested as previously described (PMID: 14597735) and single cell suspensions were generated from all three tissues. Four pools were generated per tissue. 400 viable CD4+CD8b+TCRb- cells were sorted into 8ul low-input lysis buffer containing RNaseH inhibitor, dNTPs, and 0.1% Triton X-100 in replicates. Material of 200 cells was reverse transcribed and amplified. Illumina libraries were prepared and sequenced. Results: A total of 2147 genes were differentially regulated between the different DP populations. Extrathymic DPs had 858 genes upregulated and 1284 genes downregulated compared to thymic DPs. 94 genes were commonly regulated in the two extrathymic DP subsets, whereas 23 genes were uniquely expressed in MAT DPs, 31 different genes were exclusively expressed in aortic arch DPs. Conclusion: Our study is the first to identify and provide deep transcriptional analysis two extra-thymic DP populations in mice.

2021-09-28 | GSE180582 | GEO

Promiscuity of peptides presented in HLA-DP molecules from different immunogenicity groups is associated with T-cell cross-reactivity

Project description:In the context of HLA-DP-mismatched allogeneic stem cell transplantation, mismatched HLA-DP alleles can provoke profound allo-HLA-DP-specific immune responses from the donor T-cell repertoire leading to graft-versus-leukemia effect and/or graft-versus-host disease in the patient. The magnitude of allo-HLA-DP-specific immune responses has been shown to depend on the specific HLA-DP disparity between donor and patient and the immunogenicity of the mismatched HLA-DP allele(s). HLA-DP peptidome clustering (DPC) was developed to classify the HLA-DP molecules based on similarities and differences in their peptide-binding motifs. To investigate a possible categorization of HLA-DP molecules based on overlap of presented peptides, we identified and compared the peptidomes of the thirteen most frequently expressed HLA-DP molecules. Our categorization based on shared peptides was in line with the DPC classification. We found that the HLA-DP molecules within the previously defined groups DPC-1 or DPC-3 shared the largest numbers of presented peptides. However, the HLA-DP molecules in DPC-2 segregated into two subgroups based on the overlap in presented peptides. Besides overlap in presented peptides within the DPC groups, a substantial number of peptides was also found to be shared between HLA-DP molecules from different DPC groups, especially for groups DPC-1 and -2. The functional relevance of these findings was illustrated by demonstration of cross-reactivity of allo-HLA-DP-reactive T-cell clones not only against HLA-DP molecules within one DPC group, but also across different DPC groups. The promiscuity of peptides presented in various HLA-DP molecules and the cross-reactivity against different HLA-DP molecules demonstrate that these molecules cannot be strictly categorized in immunogenicity groups.

2022-02-12 | PXD030591 | Pride

Hepatic transcriptomic profiles of mice exposed to dechlorane plus by gavage

Project description:Five-week-old male mice (Mus musculus, ICR) were exposed to dechlorane plus for 10 days. A total of tweenty-four mice were randomly assigned to control and three DP-treated groups. Six mice were applied in every group. For control group, corn oil was given to mice by gavage daily. For three DP-treated groups, mice received a daily dose of DP in corn oil at 500 mg DP /kg bw, 2000 mg DP /kg bw and 5000 mg DP /kg bw, respectively. After exposure, mice were anaesthetized under isoflurane followed by exsanguination. Livers were removed, and hepatic RAN for each mouse were immediately extract. The gene expression profiles for control and three DP-treated groups were determined by the GeneChip? Mouse Exon 1.0 ST arrays. the biological significances of differentially expressed genes (DEGs) were analyzed based on Molecule Annotation System 3.0 (MAS3.0, http://bioinfo.capitalbio.com/mas/). The microarray analysis of this study provide novel insight regarding toxicological effects and mechanism of DP at the transcriptome level

2012-09-05 | E-MEXP-3707 | biostudies-arrayexpress

Late stages of T-cell maturation in the thymus involve NF-ÎºB and tonic type I interferon signaling

Project description:Positive selection occurs in the thymic cortex, but critical maturation events occur later in the medulla. We defined the precise stage at which T cells acquire competence to proliferate and emigrate. Transcriptome analysis of late gene changes suggested roles for NF-ÎºB and interferon signaling. Mice lacking the IKK kinase TAK1, showed normal positive selection, but a specific block in functional maturation. NF-ÎºB signaling provided protection from TNF, and was required for proliferation and emigration. Alternatively, the interferon signature was independent of NF-ÎºB, and IFNÎ±R deficient thymocytes showed reduced STAT1 levels and phenotypic abnormality, but were competent to proliferate. Thus, both NF-ÎºB and tonic IFN signals are involved in the final maturation of thymocytes into naÃ¯ve T cells. Gene expression profile was performed on cells isolated from mouse thymus, including Pre-DP, Post-DP, SM&M1, M2 and Tak1-deficient SM&M1 cells.

2016-04-03 | E-GEOD-74078 | biostudies-arrayexpress

T-cell alloreactivity to HLA-DP is regulated by peptide repertoire divergence and HLA-DM mediated editing

Project description:Analysis of the peptide repertoires eluted from different HLA-DP molecules expressed in HeLa cells co-expressing Invariant chain either with or without HLA-DM as components of the HLA class II processing machinery. Divergence of the immunopeptidomes and the impact of HLA-DM were investigated in relation to the capacity of HLA-DP molecules to elicit alloreactive T-cell responses.

2022-11-21 | PXD017154 | Pride

Sox2 ablation in the DP alters its gene expression signature

Project description:Using Tbx18Cre to target embryonic DP precursors, we ablate Sox2 early and efficiently, resulting in diminished hair shaft outgrowth. Transcriptional profiling of Sox2 null DPs reveals increased Bmp6 and decreased Bmp inhibitor Sostdc1, a direct Sox2 transcriptional target. FACS sort to isolate Sox2GFP/Integrin-alpha 9 double-positive DP cells from Sox2 HET and cKO P5 skin for transcriptional profiling

2012-12-01 | E-GEOD-41597 | biostudies-arrayexpress

The role of Ternary Complex factors in T-cell Positive Selection

Project description:Removal of the transcription factor SAP1a member of the Ternary Complex Factor (TCF) group of transcription factors which in conjunction with Serum Response Factor (SRF) has been shown to have a profound effect on positive selection in the thymus. When another TCF Elk1 is knocked out in mice there is no effect on positive selection unless it is on a Sap1a KO background where the phenotype is very severe. We have stimulated isolated double positive T cells (DPs) with anti-CD3 to mimic positive selection and compared basal and stimulated transcription across the four genotypes to discover the downstream targets of Sap1a involved in positive selection. The Affymetrix mouse Chip Mouse430_2 arrays were used to define gene expression profiles in purified DPs with and with out CD3 treatment from 3 mice for each genotype (Wt,SapKO, ElkKO and SAP/Elk double KO)

2010-06-08 | E-GEOD-21546 | biostudies-arrayexpress

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