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Next generation sequencing facilitates quantitative analysis of PC9 and MTAC-P (EGFR-TKI resistant cell line derived from PC9)

ABSTRACT: The goals of this study are to compare the different transcriptome signiture between PC9 and MTAC-P with NGS-derived retinal transcriptome profiling (RNA-seq).

ORGANISM(S): Homo sapiens

PROVIDER: GSE79763 | GEO | 2019/10/29

REPOSITORIES: GEO

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Next generation sequencing facilitates quantitative analysis of MTAC-P (EGFR-TKI resistant cell line derived from PC9) with and without BCAT1 knockdown.

Project description:The goals of this study are to compare the different transcriptome signiture between MTAC-P cells with and without BCAT1 knockdown with NGS-derived retinal transcriptome profiling (RNA-seq).

2019-10-29 | GSE79764 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of s.c. tumors from nude mouse allografted by R728T1 (non-SMCs derived from Rb/P53 mouse model) with and without Taz knockdown

Project description:The goals of this study are to compare the different transcriptome signiture between s.c. tumors from nude mouse allografted by R728T1 (non-SMCs derived from Rb/P53 mouse model)with and without Taz knockdown with NGS-derived retinal transcriptome profiling (RNA-seq).

2019-07-22 | GSE84741 | GEO

Analysis of differentially expressed circRNAs after EGFR-TKI treatment

Project description:CircRNA-seq of H1975 cells treated with DMSO or Osi (500 nM) and PC9 cells treated with DMSO or Ge (100 nM) for 3 days

2022-08-26 | GSE211854 | GEO

Transcriptome analysis of PC9 cells with gefitinib or/and hypoxia treatment and comparison with gefitinib resistant PC9 cells and ALDH positive PC9 cells

Project description:Inevitable gefitinib resistance and relapse of the disease was the biggest hurdle to NSCLC treatment. Importantly, the role of hypoxia in solid tumor tissues in vivo in gefitinib acquired resistance and its relationship to lung cancer stem cells (LCSCs) has not been fully elucidated. Here, the PC9 cells were treated with short term gefitinib or/and hypoxia, also, PC9 gefitnib resistant (PC9-GR) cell line was established and ALDH positive PC9 cells were sorted by FACs. Transcriptome analysis among those PC9 cell groups revealed the important role of hypoxia in gefitinib acquired resistance and signaling transduction change, which may critical for NSCLC disease progression and recurrence.

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3' UTR RNA-seq of EGFR-mutant PC9 cells and drug-resistant clones

Project description:EGFR-mutant lung adenocarcnioma cell line PC9 pools were treated with different compounds until resistant cells regrew. Resistant and parental cells were then sequenced to study transcriptional changes.

2023-06-30 | E-MTAB-13046 | biostudies-arrayexpress

Gene expression of PC9 and PC9-OR cell line [JXQ_RNA]

Project description:To investigate the abnormal gene expression in Osimertinib Resistance lung cancer cell line, We performed gene expression profiling analysis using data obtained from RNA-seq of PC9 cell line and PC9-OR cell line.

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3' UTR RNA-sequencing of human EGFR-mutant PC9 cells that were CRISPR engineered to additionally contain EGFR-mutations T790M and C797S

Project description:Lung adenocarcinoma PC9 cells were engineered to not only contain the driving EGFR-mutations, but also EGFR T790M and EGFR C797S that provide resistance to EGFR inhibitors.

2021-07-19 | E-MTAB-9887 | biostudies-arrayexpress

scRNAseq of EGFR-mut PC9 cells control or treated for 24h or 72h with osimertinib

Project description:The experiment investigates transcriptional reponse of EGFR-mut PC9 lung cancer cells following treatment for 24h or 72h with EGFR-inhibitor osimertinib compared to control cells on a single cell level.

2021-07-19 | E-MTAB-9468 | biostudies-arrayexpress

3' UTR RNA-seq of CRISPR-edited human EGFR-mutant PC9 lung cancer cell lines after osimertinib treatment

Project description:Human EGFR-mutant lung adenocarcinoma cells (PC9) were engineered using CRISPRv2 systemt to knock-out MAVS or STING to assess impact on transcriptomic response following osimertinib treatment

2021-07-19 | E-MTAB-9885 | biostudies-arrayexpress

mRNA-seq Analysis of Transcriptomes of the PC9R and PC9 cells

Project description:The goals of this study is to compare the whole genome transcriptome of gefitinib-resistant NSCLC cell line (PC9R) with its gefitinib-sensitive counterpart (PC9) using RNA-seq tecnology Methods: Genome-wide mRNA profiles of the PC9R and PC9 cells were generated by deep sequencing, using Illumina Hiseq2000. The sequence reads that passed quality filters were analyzed in the following steps: 1) RNA-seq reads were aligned to the hg19 genome assembly using TopHat (http://bioinformatics.oxfordjournals.org/content/25/9/1105.short) with the default parameters; 2) Expression index was generated using GFOLD V1.0.9 job count (http://bioinformatics.oxfordjournals.org/content/early/2012/08/23/bioinformatics.bts515); 3) Differential expression were calculated using GFOLD V1.0.9 job diff. Gene expression was quantified in rpkm (reads per kilobase of exon per million mapped sequence reads); 4) GFOLD, a generalized fold change, was used to rank the differentially expressed genes from the RNA-seq data. The GFOLD value can be considered as a reliable log2-fold change when only a single biological replicate is available Results: We found that hundreds of genes were either down- or up-regulated in the PC9R cells compared with the PC9 cells. Specifically, 6% of the total detected genes (1487 genes) were up-regulated in the PC9R cells, with a GFOLD value over 1, and 5% of the total detected genes (1112 genes) were down-regulated, with a GFOLD value less than -1. Conclusions: Our study reveals the differentially expressed genes in gefitinib-resistant NSCLC cells comparing with the sensitive cells in a genome-wide scale. This results help to provide the novel insight into the gefitinib-resistant mechanism.

2018-03-14 | GSE74253 | GEO

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