Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effect of PHRF1 depletion on gene expression in HCT116 cells

ABSTRACT: The goal of this study was to understand how PHRF1 regulates gene expression in HCT116 cells. By conducting RNA sequencing of 3 WT and 3 KO (PHRF1 knockout) samples, we found that DNA damage response pathways were upregulated and splicing-related pathways were downregulated in KO cells versus WT cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE281702 | GEO | 2024/11/18

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Effect of PHRF1 depletion on gene expression in HeLa cells

Project description:The goal of this study was to understand how PHRF1 regulates gene expression in HeLa cells. By conducting RNA sequencing of 3 WT and 3 KO (PHRF1 knockout) samples, we found that DNA damage response pathways were upregulated and splicing-related pathways were downregulated in KO cells versus WT cells.

2024-11-18 | GSE281703 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type HCT116 and MTF1-KO HCT116 injected tumor Transcriptomes

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to use RNA-seq to find differences between WT and MTF1-KO tumor in colorectal cancer Methods: HCT116 cells and MTF1-KO HCT116 cells were injected subcutaneously into the back of NSG mice at 2x106 cells/recipient , At day 24 after injection，Tumor tissue were isolated from infected recipients，and Total RNA was collected. Besides,about 5x106 cultured HCT116 cells and MTF1-KO HCT116 cells were collected for total RNA isolation ,and sent all of them for sequencing. Conclusions: Our study represents the transcriptome difference between WT HCT116 tumor and MTF1-KO HCT116 tumor has a very positive significance for the pathological process of colorectal cancer，especially for cell adhension

2022-12-15 | GSE190435 | GEO

RNA-sequencing data of HCT116-wild type (WT), HCT116-A20 knockout (KO) and HCT116-A20-KO-rescue (OE) cells

Project description:RNA-sequencing data of HCT116-wild type (WT), HCT116-A20 knockout (KO) and HCT116-A20-KO-rescue (OE) cells

| PRJNA850418 | ENA

HCT116 cell proteome remodeling upon Torin1 treatment or amino acid withdraw. Related to Supplementary Table 1 from An et al (2020)

Project description:HCT116 cells with various genotype (WT, ATCG5 KO, RB1CC1 KO), treated with Torin1 or amino acid withdraw. TMT 11 plex single shot.

2020-07-13 | PXD017853 | Pride

Gene expression profiling of HCT116 cells with or without PHGDH knockout

Project description:HCT116 cells (WT or PHGDH KO) were harvested and mRNA were extracted for high-throughput sequencing

2021-10-31 | GSE150261 | GEO

DBC1 is a positive regulator of enhancer epigenomic writers KMT2D and p300 [HCT116 ChIP-seq]

Project description:Genome-wide maps of H3K4me3 and H3K27ac in HCT116 WT and DBC1 KO cells

2022-08-17 | GSE201362 | GEO

HCT116 MYC 3' TBE1 (WT) and KO RNA-Seq

Project description:mRNA was sequenced from HCT116 MYC 3' TBE1 (WT) and KO cells to identify genes differentially expressed after deletion of the MYC 3' TBE1

2016-05-24 | GSE70833 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of TP53-WT and TP53-KO HCT116 cells transcriptomes [RNA-seq]

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare TP53-WT and TP53-KO HCT116 cells transcriptome profiling (RNA-seq) under 5-FU treatment condition and to evaluate the correlation between transcriptome profileing and chromatin accessibility under 5-FU treatment. Methods: HCT116 cell profiles of TP53-WT and TP53- KO were generated by deep sequencing, in duplicates, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform levels: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA). Conclusions: Our study represents the detailed analysis of TP53-WT and TP53-KO HCT116 cell transcriptomes under 5-FU treatment with different timepoint, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that RNA-seq offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a TP53-WT and TP53-KO cells with and without 5-FU treatment in different timepoint. We conclude that NGS based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

2021-02-10 | GSE157951 | GEO

Expression profiles of HCT116 colorectal cancer cells and HCT116-derived CDKN1A (p21) knockout (ko) cells.

Project description:Gene expression profiles were obtained via Nanostring nCounter Expression Assay (PanCancer Progression Panel, Nanostring Technologies, Hamburg, Germany). We aimed to obtain a gene expression signature associated to the kockout of p21 (i.e. Cyclin Dependent Kinase Inhibitor 1A, CDKN1A) in colorectal carcinoma samples and its association with of epithelial-mesenchymal transition (EMT). We analysed and compared three independent cultures of HCT116 p21 wt cells and three HCT116 p21-/- ko cells.

2019-11-01 | GSE135923 | GEO

Unirradiated HCT116-Clone2 cells

Project description:cDNA microarray study of unirradiated X-radiation (XR) resistant HCT116-Clone2 cells versus unirradiated HCT116-Clone10 cells. HCT116-Clone10 cells have similar XR response with parental HCT116 cells. Keywords: repeat sample

2004-06-04 | GSE798 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data