Similar Datasets
Project description:Difference gene analysis in K562 cells
| PRJNA752375 | ENA
Project description:LncRNA-IIRX plays critical role in Bcr-Abl-induced tumorigenesis. To discover its mechanisms underlying cellular transformation by Bcr-Abl oncogene, genome-wide mRNA expression was measured by RNA-seq in K562 cells expressing shRNA targeting lncRNA-IIRX and control cells. We identified many genes with differential expression in K562 cells after knocking down lncRNA-IIRX.
2019-04-17 | GSE120337 | GEO
Project description:Purpose: The aim of this study was to evaluate the difference of mRNA and lncRNA in K562 cells treated with vandetanib (1.56 μM) and control (DMSO) by high-throughput sequencing results. Methods: Total RNA was extracted using the RNAfast200 kit according to the manufacturer’s protocol. Then, 200 ng RNA was sequenced with high throughput, and then pathway and GO analysis were used for comprehensive analysis. Finally, RT-PCR method was used to validate in large sample population. Results: High-throughput sequencing results showed that there were significant differences in mRNA and lncRNA in K562 cells treated with vandetanib (1.56 μM) and control (DMSO). Conclusions: It is the first time that we have used high-throughput sequencing to study the difference of mRNA and lncRNA in K562 cells treated with vandetanib (1.56 μM) and control (DMSO). The results of sequencing show that the expression of mRNA and lncRNA is quite different in K562 cells treated with vandetanib (1.56 μM) and control (DMSO).
2020-09-25 | GSE158518 | GEO
Project description:We previously characterized zinc finger protein gene HZF1 (ZNF16) and demonstrated its important roles in erythroid and megakaryocytic differentiation of K562 cells by loss-function assay. However its effect in erythroid and megakaryocytic differentiation of hematopoietic stem/progenitor cells (HSPCs) and the mechanisms by which it functions have not been understood. In this study, we detected up-regulation of ZNF16 during erythroid and megakaryocytic differentiation of K562 cells and normal CD34+ HSPCs, and demonstrated that ZNF16 promotes erythroid and megakaryocytic differentiation by gain-of-function and loss-of-function experiments. Gene expression profiling by mRNA array and PCR validation in the K562 transforments with ZNF16 over-expression suggested that cell division cycle-associated 7-like gene (JPO2) and v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog gene (c-KIT) were among the genes regulated possibly by ZNF16. Luciferase reporter assay and Chromatin Immunoprecipitation demonstrated that ZNF16 binds to JPO2 and c-KIT promoters and inhibits their expression in K562 cells. A significant decrease of JPO2 and c-KIT levels was observed during erythroid and megakaryocytic differentiation of K562 and CD34+ cells. The knockdown of either JPO2 or c-KIT partially rescued the differentiation inhibition caused by ZNF16 knockdown. We also found that ZNF16 inhibits c-KIT/c-Raf/MEK/ERK/c-Jun/HEY1 signal pathways, which finally up-regulated expression of GATA1, a central regulator of erthroid and megakaryocyte differentiation. By lentivirus-mediated gene transfer, we demonstrated that enforced expression and knockdown of ZNF16 in HSPCs down-regulated and up-regulated expression of its targets respectively. Our data collectively demonstrate that ZNF16 promotes erythropoiesis and megakaryocytopoiesis via its regulation on JPO2 and c-KIT. 4 samples are analyzed, H4-1 and H4-2 are two stable K562 transductants with ZNF16 over-expression, PC1 and PC2 are stable control K562 transductants. Stable K562 transductants were obtained for RNA extraction and hybridization on an Illumina HumanHT-12 V4.0 expression beadchipe xpression Array platform.
2016-03-29 | E-GEOD-46593 | biostudies-arrayexpress
Project description:K562-shX cells are made in an effort to validate TFBS data and ChIP-seq antibodies in Myers lab (GSE32465). K562 cells are transduced with lentiviral vector having Tet-inducible shRNA targeting a transcription factor gene. Cells with stable integration of shRNA constructs are selected using puromycin in growth media. Doxycycline is added to the growth media to induce the expression of shRNA and a red fluorescent protein marker. A successful shRNA cell line shows at least a 70% reduction in expression of the target transcription factor as measured by qPCR. For identification, we designated these cell lines as K562-shX, where X is the transcription factor targeted by shRNA and K562 denotes the parent cell line. For example, K562-shATF3 cells are K562 derived cells selected for stable integration of shRNA targeting the transcription factor ATF3 gene and showed at least a 70% reduction in the expression of ATF3 gene when measured by qPCR. Cells growing without doxycycline (uninduced) are used as a control to measure the change in expression of target transcription factor gene after induction of shRNA using doxycycline. For detailed growth and culturing protocols for these cells please refer to http://hudsonalpha.org/sites/default/files/pdf/shRNA%20K562%20protocol.pdf. To identify the potential downstream targets of the candidate transcription factor, analyze the mRNA expression profile of the uninduced and induced K562-shX using RNA-seq. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Make K562-shX cells as described in the http://hudsonalpha.org/sites/default/files/pdf/shRNA%20K562%20protocol.pdf. Measure the mRNA expression levels in uninduced K562-shX and induced K562-shX cells in two biological replicates using RNA-seq. Identify the potential downstream targets of the candidate transcription factor.
2011-12-01 | E-GEOD-33816 | biostudies-arrayexpress
Project description:Stau2 knockdown in human bcCML cells (K562)"
| PRJNA557137 | ENA
Project description:Summary: Ribonuclease Inhibitor (RI also known as Rnh1) is a 50 kDa, ubiquitously expressed leucine-rich repeat (LRR) protein. It is localized in cytosol and binds to pancreatic-type ribonucleases and inhibit their function. However, the entire biological role for Rnh1 is unknown. We generated RNH1 knock out K562 cells by CRISPR/Cas9 method. Here we studied differential gene expression from wild type and RNH1 knock out K562 cells by RNA-Seq analysis. Overall design: Total RNA was isolated from wild type and RNH1 deficient K562 cells.
2017-03-05 | E-MTAB-5162 | biostudies-arrayexpress
Project description:Interventions: Gold Standard:tissue or cytopathology;Index test:secreted LncRNA
Primary outcome(s): Differential expression of LncRNA in peripheral blood exosomes of patients
Study Design: Single arm
| 2739486 | ecrin-mdr-crc
Project description:We identified long noncoding RNAs (lncRNAs) expressed in macrophages and characterized one lncRNA, designated lncFAO. To analyze the function of lncFAO, effects of knockdown and knockout of lncFAO were analyzed by RNA-seq.
2020-07-08 | GSE129961 | GEO
Project description:Genomic profiling of K562 cells resistant to imatinib as well as imatinib resistant CML patients harboured a recurrent chromosomal amplification in 8q11.2-12.1. Gene encoding PLAG1, a transcription factor associated with cancers and chemo resistance, resides on this locus and was found to be amplified in resistant cells. Upon PLAG1 knockdown we observed a decrease in imatinib resistance, and to understand the molecular events underlying PLAG1-mediated imatinib resistance, RNA sequencing was carried out. Imatinib-resistant K562 cells were transfected with lentiviral particles containing shRNA against PLAG1 and lentiviral particles containing pLKO.1-empty vectors. Monoclonal populations were established. Total RNA sequencing was performed. For QC, RNA samples were quantified using the Qubit RNA BR Assay kit (Invitrogen, Cat# Q10211). RNA purity was checked using QIAxpert, and RNA integrity was assessed on TapeStation using High Sensitivity RNA ScreenTape® (Agilent, Cat# 5067-5579). QC passed RNA samples were subjected to the library preparation, and NEB Ultra RNA-Seq Library Prep kit protocol (Cat# E7530L) was used and sequenced on Illumina NovaSeq 6000 instrument. Transcriptomic analysis identified several genes down-regulated upon PLAG1 knockdown which were further investigated.
2024-01-01 | E-MTAB-11893 | biostudies-arrayexpress