Ontology highlight
ABSTRACT:
PROVIDER: PRJNA628570 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To investigate MMP10 downstream targets involved in the regulation of tongue cancer metastasis, transcriptome sequencing of MMP10 overexpression (AW13516) and knockdown clones (AW8507 and CAL27) was performed. 1) For stable overexpression of MMP10 in AW13516 cell line, pBABEpuro-MMP10 construct was used. pBABE-puro empty vector was used as control for overexpression. Transfection was carried out using lipofectamine kit (Cat No. L3000015, Invitrogen) in 293FT cells and virus was collected after 48 hours. AW13516 cells were infected with viral particles to generate stable MMP10-overexpression or vector control clones. Stable MMP10-overexpression clones generated and used for RNA-seq are: a) AW13516-vector control; b) AW13516-MMP10 overexpression clones. 2) For shRNA mediated stable knockdown of MMP10 in CAL27 and AW8507 cell lines, 3 lentiviral shRNA constructs targeting MMP10 were used. A short hairpin non-targeting (sh-NT) construct was used as vector control. Transfection and infection with viral particles was performed as described in the overexpression study. Stable MMP10-knockdown clones generated and used for RNA-seq are: a) AW8507 shRNA-NT vector control, b) AW8507 MMP10 shRNA-1, c) AW8507 MMP10 shRNA-2, d) AW8507 MMP10 shRNA-3, e) CAL27 shRNA-NT vector control, f) CAL27 MMP10 shRNA-1, g) CAL27 MMP10 shRNA-2, h) CAL27 MMP10 shRNA-3. To identify the differentially expressed genes, cuffdiff and NOISeq tools were used, and overlapping significantly differentially expressed genes (-1.5<log2FC>1.5; p-value<0.05 or prob>0.95) were identified for further characterization.
2023-01-04 | E-MTAB-11185 | biostudies-arrayexpress
Project description:In this study, we aim to analyze the role and mechanism of transcription factor KLF7 in oral cancer. We used CHIP-seq to analyze the binding sites of KLF7 on the genome of oral cancer cell line CAL27 Meanwhile, we also analyzed the changes in gene expression after CAL27 overexpression of KLF7 using transcriptome sequencing
2025-02-01 | GSE285330 | GEO
Project description:The aim of this study is to compare the CGA Knockdown multi-drug resistant (MDR) cells (SGC7901/ADR and SGC7901/VCR) to the control cells. The total RNA of the indicated cells were extracted using Qiagen RNA Extraction Kit and RNA sequencing was performed. Significant differences in genes and signaling pathways were found between CGA knockdown and control MDR cells. This study provides a basis for applying RNA sequencing techniques to characterize targets in MDR cells.
2022-03-30 | GSE193739 | GEO
Project description:To study if non-invasive oral squamous cell carcinoma (OSCC) cells can acquire mechanical memory from stiff matrix and investigate the role of cell contractility in that process, Cal27 were conditioned (for 5 days) either by matrix stiffness or by direct modulation of cell contractility and then replated to a new niche lack of sources for the cells to learn. Cal27 with different types of conditioning were categorized either "Learn" or "Don't Lean/Forget" based on the existence of mechanical memory. Comparative gene expression profiling was done between "Learn" vs. "Don't Learn/Forget" Cal27 groups by RNA sequencing
2023-04-07 | GSE207685 | GEO
Project description:To gain insight into the alterations of gene expression profile in the course of non-mutationally acquired resistance, we performed RNA-seq comparing MDR persister cells to MDR cancer cells.
2021-11-04 | GSE187441 | GEO
Project description:In this study, we aim to analyze the role and mechanism of transcription factor KLF7 in oral cancer. We used CHIP-seq to analyze the binding sites of KLF7 on the genome of oral cancer cell line CAL27 Meanwhile, we also analyzed the changes in gene expression after CAL27 overexpression of KLF7 using transcriptome sequencing
2025-02-01 | GSE285331 | GEO
Project description:Purpose: Investigate whether maculopapular drug rash with COVID-19 infection (COVID19-MDR) exhibits a distinct gene expression in the skin as compared to non-COVID19-MDR. Methods:RNA was extracted from formalin-fixed, paraffin-embedded (FFPE) skin biopsies from COVID-MDR (n=3), MDR (n=7), and Healthy control (n=5). Library preparation for RNA-seq was performed by using the TruSeq Stranded RNA library preparation kit including polyA enrichment (Illumina) from total RNA. Sequencing was performed on the the Illumina NextSeq 500 platform with 75 cycles. Results: RNA sequencing from lesional skin showed that pathways of cytolysis and eosinophil chemotaxis were activated in COVID MDR. Cytolysis/cellular defense response related genes, such as PRF1 (perforin), GZMA (Granzyme A) and GNLY (Granulysin), as well as eosinophil migration/lymphocyte chemotaxis genes, e.g. C-C Motif chemokine ligand 5 (CCL5), CCL13, were upregulated in COVID MDR. Conclusions: This study provide an opportunity to understand the pathogenesis of MDR with the COVID-19 infection. We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.
2021-07-03 | GSE161225 | GEO
Project description:Multidrug resistance (MDR) frequently develops in cancer patients exposed to chemotherapeutic agents and is usually brought about by over-expression of P-glycoprotein (P-gp) which acts as a drug efflux pump. MiRNAome profiling using next-generation sequencing identified differentially expressed microRNAs (miRs) between parental K562 cells and MDR K562 cells (K562/ADM) induced by chronic adriamycin treatment.
2013-10-29 | GSE51774 | GEO
Project description:Subsequently, using a combination of BSA-seq, transcriptomic sequencing (RNA-seq), and proteomic sequencing approaches, we identified the candidate gene Nitab4.5_0008674g0010 that encodes dihydroneopterin aldolase as a factor associated with tobacco leaf yellowing.
2024-06-15 | PXD053162 |