Effect of site directed mutagenesis on transcriptomic difference between H460 (T/T) and H460 (C/C) cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE213199 | GEO | 2023/05/10
REPOSITORIES: GEO
Similar Datasets
Project description:To study the effect of rs1663689 on lung cancer cells, we generated A549(C/C) from A549(T/T) using CRISPR/Cas9 technology and performed RNA-seq.
2023-05-10 | GSE225330 | GEO
Project description:We generated H460 cells with acquired TRAIL resistance by exposing the parental sentisitve cells to subtoxic concentrations of TRAIL for 6 months. Then we compared the microRNA expression profile in the sensitive versus resistant cells. H460 cells were treated with subtoxic concentrations of TRAIL for 6 month. After confirmation of the resistance, the RNA was extracted and the microRNA expression profile was analyzed using the NanoString technology.
2014-09-01 | E-GEOD-55821 | biostudies-arrayexpress
Project description:Comparing genome-wide gene expression profiles of highly metastatic lung cancer cell line NCI-H460-LNM35 vs low metastatic parental clone NCI-H460-N15 Keywords: Expression profiling with cDNA microarray
2010-08-21 | GSE16649 | GEO
Project description:BACKGROUND: Cancer stem-like cells were isolated from human H460 non-small cell lung cancer cells by limiting dilution assays and by their holoclone morphology, followed by assessment of their self-renewal capacity, tumor growth, vascularity, and tumor blood perfusion. H460 holoclones were used to implant H460 holoclone-derived tumors, which grew slower than parental H460 tumors, but displayed significant increases in microvessel density and tumor blood perfusion. Microarray analysis identified differentially regulated genes in the holoclone-derived tumors, of which many were associated with angiogenesis. The differentially regulated genes include several small leucine-rich proteoglycans that may modulate angiogenesis and serve as novel therapeutic targets for inhibiting cancer stem cell-driven angiogenesis.(Cancer Letters Vol 346, Issue 1, 28 April 2014, Pages 63M-bM-^@M-^S73; PMID: 24334139; PMCID: PMC3947657). Implanted tumors derived from H460 parental cells, or from each of four independent H460 holoclones, were implanted subcutaneously in scid immunodeficient mice. Tumors derived from the 4 holoclones (designated H460/2E1, H460/2H3, H460/3F1, and H460/2E7) were used for global transcriptome/microarray analysis in direct comparison to H460 tumors grown from parental H460 cells. For each H460 holoclone-derived tumor line or H460 parental cell-derived tumor, total RNA was prepared from n=7 to n=10 individual tumors and used to prepare two independent pools of tumor RNA (each pool comprised of RNA isolated n=3-5 tumors) for use in a two color microarray analysis. Tumor RNA pools were prepared by combining equal amounts of RNA from each individual tumor to minimize the impasct of inter-tumoral variation on gene expression profiles. All RNAs had an RNA integrity number >8.0, determined using an Agilent Bioanalyzer 2100 instrument. cDNAs transcribed from pools of RNA for each holoclone-derived tumor line and for each parental H460 cell-derived tumor pool, were labeled with Alexa 647 or Alexa 555 dyes in a fluorescent reverse pair (dye swap) design for competitive hybridization to Agilent Whole Human Genome Microarrays.
2014-04-23 | E-GEOD-57000 | biostudies-arrayexpress
Project description:Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications, H3K27ac, H3K4me3, H3K27me3 and H3K9me3 in H460 (T/T) and H460 (C/C) cells
2023-05-10 | GSE213197 | GEO
Project description:Transcription profile of cancer stem cells isolated from human non-small cells lung cancer (NSCLC) H460 cells. The profile of H460 cells that were made resistant to cisplatin after a single treatment with the drug was also determined. Both profiles were finally compared. Each microarray contained one of these comparative experiments (two-channels): H460C (H460 derived CSCs) vs H460 and H460R (cisplatin-resistant H460 cells) vs H460. Technical replicates were made with dye-swap-based design. Total biological replicates per cell type (H460C and H460R): 2.
2014-07-30 | E-GEOD-54981 | biostudies-arrayexpress
Project description:BACKGROUND: Cancer stem-like cells were isolated from human H460 non-small cell lung cancer cells by limiting dilution assays and by their holoclone morphology, followed by assessment of their self-renewal capacity, tumor growth, vascularity, and tumor blood perfusion. H460 holoclones were used to implant H460 holoclone-derived tumors, which grew slower than parental H460 tumors, but displayed significant increases in microvessel density and tumor blood perfusion. Microarray analysis identified differentially regulated genes in the holoclone-derived tumors, of which many were associated with angiogenesis. The differentially regulated genes include several small leucine-rich proteoglycans that may modulate angiogenesis and serve as novel therapeutic targets for inhibiting cancer stem cell-driven angiogenesis.(Cancer Letters Vol 346, Issue 1, 28 April 2014, Pages 63–73; PMID: 24334139; PMCID: PMC3947657).
2014-04-23 | GSE57000 | GEO
Project description:Purpose: The goal of this study is to compare the gene expression profiles of H460, H460-ERT2-RUNX3-WT and H460-ERT2-RUNX3-MT(K94/171R) cells. Methods: H460, H460-ERT2-RUNX3 WT, and H460-ERT2-RUNX3-MT(K94/171R) cells were serum-starved for 24 hr, and then stimulated with 10% serum or 10% serum + 1 uM 4-OHT for 0, 8, or 16 hr. RNA was extracted from the cells. Isolated total RNA was processed for preparation of an RNA-seq library using the Illumina TruSeq Stranded mRNA Sample Preparation kit (Illumina, San Diego, CA, USA). Quality and size of libraries were assessed using the Agilent 2100 Bioanalyzer DNA kit (Agilent, Santa Clara, CA, USA). All libraries were quantified by qPCR using a CFX96 Real Time System (Bio-Rad, Hercules, CA, USA) and sequenced on NextSeq500 sequencers (Illumina). Sequencing adapters and low-quality bases in the raw reads were trimmed using the Cutadapt software. The cleaned high-quality reads were mapped to the human reference genome hg19 (https://genome.ucsc.edu) using STAR software. Genes differentially expressed between two selected biological conditions were identified by Cuffdiff in the Cufflinks package (http://cole-trapnell-lab.github.io/cufflinks/papers/). Results: RNA-Sequencing Data suggest that the R-point defends against oncogenic K-RAS–induced tumorigenesis not only by regulating intracellular programs (cell cycle, apoptosis, and metabolic pathways), but also by regulating extracellular programs (inflammatory response and immune response).
2019-03-13 | GSE128174 | GEO
Project description: Not available
| S-EPMC4432289 | biostudies-literature
Project description:The CRISPR-Cas9 system enables efficient sequence-specific mutagenesis for creating germline mutants of model organisms. Key constraints in vivo remain the expression and delivery of active Cas9-guideRNA ribonucleoprotein complexes (RNPs) with minimal toxicity, variable mutagenesis efficiencies depending on targeting sequence, and high mutation mosaicism. Here, we established in vitro-assembled, fluorescent Cas9-sgRNA RNPs in stabilizing salt solution to achieve maximal mutagenesis efficiency in zebrafish embryos. Sequence analysis of targeted loci in individual embryos reveals highly efficient bi-allelic mutagenesis that reaches saturation at several tested gene loci. Such virtually complete mutagenesis reveals preliminary loss-of-function phenotypes for candidate genes in somatic mutant embryos for subsequent generation of stable germline mutants. We further show efficient targeting of functional non-coding elements in gene-regulatory regions using saturating mutagenesis towards uncovering functional control elements in transgenic reporters and endogenous genes. Our results suggest that in vitro assembled, fluorescent Cas9-sgRNA RNPs provide a rapid reverse-genetics tool for direct and scalable loss-of-function studies beyond zebrafish applications.
2016-05-01 | E-MTAB-4143 | biostudies-arrayexpress