Similar Datasets
Project description:We used scRNA-Seq to examine BCC immune cell heterogeneity.
2023-03-29 | GSE204949 | GEO
Project description:We used scRNA-Seq to examine BCC tumor heterogeneity.
2022-10-25 | GSE186183 | GEO
Project description:Activation of the Sonic hedgehog (Shh) signaling pathway due to Patched 1 (PTCH1) mutation is a key event in sporadic and familial basal cell carcinoma (BCC) development. To find out the specific pathway for therapeutic intervention, we developed a mouse BCC model by skin specific Ptch1 inactivation, and sought to identify novel Shh targets. We used microarrays to identify up-regulated genes in mouse BCC. We used microarrays to identify down-regulated genes in mouse BCC cell line by cyclopamine.
2018-01-15 | GSE20065 | GEO
Project description:In summary, we have validated differential expression of several miRs, namely two that are downregulated in all BCC subtypes compared to control skin (miR.383.5p, miR.145.5p), two that are downregulated in superficial BCC (miR.181c.5p, miR.181b.5p) relative to nodular and infiltrative BCC, and several that are upregulated in infiltrative BCC relative to superficial BCC (miR.22.5p, miR.18a.3p, miR.708.5p, miR.758.3p, miR.30c.5p), and two that are upregulated in infiltrative BCC relative to nodular BCC (miR.22.5p, miR.758.3p). To our knowledge, this study has investigated and validated the largest number of BCC tumors representing the different subtypes.
2024-01-01 | GSE245676 | GEO
Project description:Punch biopsies from patients with BCC (n=3) and non-lesional skin (n=3) were included in the study. Microarray based circRNA expression profiles were acquired using Arraystar circRNA Arrays V. 2.0 screening for 13,617 distinct human circRNA candidates. We identified circRNAs differentially expressed in BCC compared to non-lesional skin (control).
2016-04-21 | GSE74756 | GEO
Project description:A total of 3 patients with basal cell carcinoma (BCC) and 3 healthy individuals (control; non-lesional skin) were enrolled in the study. Punch biopsies (4 mm) were obtained under local anaesthesia and immediately put in RNAlater (Qiagen, Hilden, Germany) and stored at - 80 °C until RNA extraction. The lncRNA and mRNA expression in BCC was compared to lncRNA and mRNA expression in non-lesional skin (control).
2016-03-29 | E-GEOD-74858 | biostudies-arrayexpress
Project description:Single cell sequencing technology has been widely used for understanding the heterogeneity of complex tissue and for identifying novel cell types or cell states. Previous efforts of single cell profiling are mostly performed by measuring transcriptomes using single cell RNA sequencing (scRNA-seq). scRNA-seq is relatively well developed and around 500 analysis tools are currently available for performing different tasks. In the past five years, assays for profiling the single cell chromatin accessibility landscape have emerged and provide extra information about gene regulation at the epigenetic level. Due to its simplicity and sensitivity, single cell Assays for Transposase-Accessible Chromatin using sequencing (scATAC-seq) is widely used to obtain chromatin accessibility. This data will be used to comprehensively evaluate scATAC-seq data analysis tools and gaps in analysis workflows together with publicly available bulk ATAC-Seq and scATAC-seq data using optimised universal evaluation metrics.
2024-01-10 | GSE223319 | GEO
Project description:Imiquimod is a Toll-like receptor (TLR)-7 agonist capable of inducing complete clearance of basal cell carcinoma (BCC) and other cutaneous malignancies. We hypothesized that the characterization of the early transcriptional events induced by imiquimod may provide insights about immunological events preceding acute tissue and/or tumor rejection. We report a paired analysis of adjacent punch biopsies obtained pre- and post-treatment from 36 patients with BCC subjected to local application of imiquimod (N = 22) or vehicle cream (N=14) in a blinded, randomized protocol. Four treatments were assessed (q12 applications for 2 or 4 days, or q24 hrs for 4 or 8 days). RNA was amplified and hybridized to 17.5K cDNA arrays. All treatment schedules similarly affected the transcriptional profile of BCC; however, the q12 X 4days regimen, associated with highest effectiveness, induced the most changes with 637 genes unequivocally stimulated by imiquimod. A minority of transcripts (98 genes) confirmed previous reports of interferon-Â involvement. The remaining 539 genes portrayed additional immunological functions predominantly involving the activation of cellular innate and adaptive immune-effector mechanisms. Importantly, these effector signatures recapitulate previous observations of tissue rejection in the context of cancer immunotherapy, acute allograft rejection and autoimmunity. This study based on a powerful and reproducible model of cancer eradication by innate immune mechanisms provides the first insight in humans of the early transcriptional events associated with immune rejection. This model is likely representative of constant immunological pathways through which innate and adaptive immune responses combine to induce tissue destruction. Keywords: compound treatment design We report a paired analysis of adjacent punch biopsies obtained pre- and post-treatment from 36 patients with BCC subjected to local application of imiquimod (N = 22) or vehicle cream (N=14) in a blinded, randomized protocol. Four treatments were assessed (q12 applications for 2 or 4 days, or q24 hrs for 4 or 8 days). RNA was amplified and hybridized to 17.5K cDNA arrays.
2006-10-04 | E-GEOD-5121 | biostudies-arrayexpress
Project description:Single cell ATAC-seq (scATAC-seq) was performed on macaque embryonic stem cell-derived cerebral organoids. scATAC-seq was performed on day 60 (2 months old cerebral organoid).
2019-10-16 | E-MTAB-8087 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below.
2022-10-25 | GSE186184 | GEO