Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Quantitative Analysis of Scramble control and LncRNA HMRHL siRNA knockdown in chronic myelogenous leukemia (CML) K562 Cell lines transcriptome profile

ABSTRACT: The goals of this study are to compare differentianl gene expression between Scramble control and knockdown of HMRHL in K562 cell lines. Subsequently to determine the cellular pathway and biological process affected most upon HMRHL silencing from NGS-derived K562 cells transcriptome profiling (RNA-seq).

ORGANISM(S): Homo sapiens

PROVIDER: GSE167440 | GEO | 2021/03/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Quantitative Analysis of Scramble control and LncRNA HMRHL siRNA knockdown in chronic myelogenous leukemia (CML) K562 Cell lines transcriptome profile

Project description:Quantitative Analysis of Scramble control and LncRNA HMRHL siRNA knockdown in chronic myelogenous leukemia (CML) K562 Cell lines transcriptome profile

| PRJNA704657 | ENA

A novel small-molecule inhibitor of STAT5A/STAT5B with therapeutic potential for prostate cancer and CML

Project description:We assessed the gene expression profiles induced by both genetic and pharmacological knockdown of Stat5a/b in CML cells. Stat5 was suppressed in K562 cells by lentiviral expression of Stat5 shRNA vs. scramble control for 6 days or by treatment of the cells with IST5-002 (5 µM) for 48 h. K562 cells were treated with IST5-002 (5 µM) or vehicle (DMSO) for 48 h. For Stat5 knockdown, K562 cells were infected with Stat5-shRNA lentivirus or scramble-shRNA lentivirus (as control) for 48 h followed by puromycin (2ug/ml) selection for 6 days to enrich for cells expressing Stat5 or scramble shRNA. Each group (vehicle control, IST5-002, scramble-shRNA control and Stat5-shRNA) was prepared in triplicate, and RNA samples from each group were not pooled.

2015-07-01 | E-GEOD-61312 | biostudies-arrayexpress

Expression analysis of C2C12 cells treated with scramble siRNA or siRNA directed against Fndc1

Project description:We transfected C2C12 cells with 100nM of scrambled siRNA scramble and an siRNA directed against Fndc1. Cells were harvested at 48h post-transfection and RNAseq was performed with polyA selection

2024-08-17 | GSE217125 | GEO

Expression analysis of C2C12 cells treated with scramble siRNA or siRNA directed against Brd4

Project description:We transfected C2C12 cells with 100nM of scrambled siRNA scramble and an siRNA directed against Brd4. Cells were harvested at 48h post-transfection and RNAseq was performed with polyA selection

2022-09-28 | GSE141777 | GEO

PRC SiRNA vs scramble transfection in XTC.UC1 cells

Project description:PGC-1 related coactivator (PRC) shares structural and functional features with PGC-1{alpha}. It regulates several metabolic pathways and mitochondrial biogenesis. Its specific role in the early programming of cell proliferation suggests a finely regulated crosstalk between the mitochondrial functions and the cell cycle status. To explore the PRC-regulated pathways, we used a cell-line model of mitochondrial-rich tumors, presenting an oxidative metabolism and a specific increase in PRC expression. Microarray studies of temporal PRC invalidation in these XTC.UC1 cells were compared to the functional status of the mitochondria as well as to the expression level of genes and proteins involved in the oxidative phosphorylation process. Compared with what was observed for PGC-1{alpha}, we explored the role of nitric oxide in the PRC-regulated mitochondrial biogenesis. We proved that nitric oxide rapidly influences the expression of PRC at the transcriptional level. Focusing on mitochondrial energy metabolism, we demonstrated that PRC differentially controls the respiratory chain complexes and the coupling efficiency, in order to conserve a sufficient level of ATP and to protect the cell from oxidative stress. Our results highlight the key role of the PRC coactivator in the fine modulation of metabolic functions in response to the cell cycle status. Keywords: Transcriptionnal coactivator invalidation by SiRNA Expression profiles at 0h, 12h, 24h and 48h of PRC SIRNA treatment compared to scramble and referred to time of 20% serum induction. Expression profiles of PRC SIRNA and scramble during serum starvation were referred as -1.

2010-05-14 | E-GEOD-14282 | biostudies-arrayexpress

A novel small-molecule inhibitor of STAT5A/STAT5B with therapeutic potential for prostate cancer and CML

2015-07-01 | GSE61312 | GEO

Scramble and Brown fat lncRNA 1 knockdown (shBlnc1) expressing differentiated brown adipocyte

Project description:Blnc1 is a novel nuclear lncRNA that promotes brown and beige adipocyte differentiation and function. Blnc1 forms a ribonucleoprotein complex with transcription factor EBF2 to stimulate the thermogenic gene program. Further, Blnc1 itself is a target of EBF2, thereby forming a feedforward regulatory loop to drive adipogenesis toward thermogenic phenotype. We used microarrays to elucidate the role of Blnc1 on brown adipocyte differentiation and mitochondrial function. Brown adipocytes expressing Scramble or brown fat lncRNA 1 knockdown (shBlnc1) were differentiated for 6 days and harvested for RNA isolation and microarray using Affymetrix Mouse MG-430 PM Strip arrays. Two replicated samples were included in this study.

2015-02-28 | E-GEOD-57540 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of Ctrl-siRNA and c-Myc-siRNA cells' Transcriptomes in lymphoma

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analysis the differiational genes and pathways in Ctrl-siRNA and c-Myc-siRNA lymphoma cells by using NGS-derived lymphoma transcriptome profiling (RNA-seq). Methods: Ctrl-siRNA and c-Myc-siRNA cells' mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with following methods: Alignment by using HISAT2 v2.1, IGV was used to to view the mapping result by the Heatmap, histogram, scatter plot or other stytle, FPKM was then calculated to estimate the expression level of genes in each sample, DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates and Function Enrichment Analysis including GO enrichment analysis and KEGG . Conclusions: Our study represents the first detailed analysis of Ctrl-siRNA and c-Myc-siRNA cells' transcriptomes, 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 NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

2020-10-02 | GSE126739 | GEO

RNA-seq quantification in EPS15 knockdown and scramble-oligo controls in JEG3 cells

Project description:Purpose: The goals of this study are to compare transcriptomic profiles of JEG-3 cells in EPS15 knockdown and control cells. Methods: EPS15 scramble oligos were used as a negative control, while an siRNA targetting EPS15 was used to generate knockdown cell lines. Results: Using an optimized data pipeline, we quantified mRNA expression of 37,788 genes and detected differentially-expressed genes across knockdown and control cell lines. Conclusions: Our results provide some experimental evidence that EPS15 has transcriptomic consequences in human placenta-derived JEG3 cells.

2021-10-07 | GSE185071 | GEO

miRNA expression profiles of PRC SiRNA vs scramble transfected XTC.UC1 cells

2011-11-22 | E-GEOD-33843 | biostudies-arrayexpress