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Transcriptomic profiling of human BLaER1 pre-B cells transdifferentiation into macrophages

ABSTRACT: Transcriptomic profiling of human BLaER1 pre-B cells transdifferentiation into macrophages

PROVIDER: PRJEB41520 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR4872770_1.fastq.gz	Fastqsanger.gz
	ERR4872770_2.fastq.gz	Fastqsanger.gz
	ERR4872780_1.fastq.gz	Fastqsanger.gz
	ERR4872780_2.fastq.gz	Fastqsanger.gz
	ERR4872771_1.fastq.gz	Fastqsanger.gz

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Transcriptomic profiling of human BLaER1 pre-B cells transdifferentiation into macrophages

Project description:BLaER1 is a human B cell precursor leukemia cell line derived from the RCH-ACV cells. These cells are stably infected with a construct that overexpresses the transcription factor C/EBPa fused with the estrogen receptor hormone binding domain (ER) and GFP. Upon induction with beta-estradiol, C/EBP is internalized into the nucleus, promoting massive transcriptional changes and inducing the transdifferentiation of these pre-B cells into functional macrophages. This process, that lasts 7 days, can be monitored by the detection of specific B cell and macrophage surface markers by flow cytometry. With the goal of understanding the interplay between chromatin and transcription, we have generated transcriptomic data by RNA-Seq in twelve time points along the transdifferentiation process, in two biological replicates.

2022-05-31 | E-MTAB-9790 | biostudies-arrayexpress

Epigenetics profiling of human BLaER1 pre-B cells transdifferentiation into macrophages

Project description:BLaER1 is a human B cell precursor leukemia cell line derived from the RCH-ACV cells. These cells are stably infected with a construct that overexpresses the transcription factor C/EBPa fused with the estrogen receptor hormone binding domain (ER) and GFP. Upon induction with beta-estradiol, C/EBP is internalized into the nucleus, promoting massive transcriptional changes and inducing the transdifferentiation of these pre-B cells into functional macrophages. This process, that lasts 7 days, can be monitored by the detection of specific B cell and macrophage surface markers by flow cytometry. With the goal of understanding the interplay between chromatin and transcription, we have obtained the epigenetic profile of 9 histone modifications (H3K4me1, H3K4me2, H3K4me3, H3K9ac, H3K27ac, H3K36me3, H4K20me2, H3K9me3 and H3K27me3) by ChIP-Seq in twelve time points along the transdifferentiation process, in two biological replicates.

2022-05-31 | E-MTAB-9825 | biostudies-arrayexpress

Epigenetics profiling of human BLaER1 pre-B cells transdifferentiation into macrophages

Project description:Epigenetics profiling of human BLaER1 pre-B cells transdifferentiation into macrophages

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Epigenetic analysis of BlaER1 transdifferentiation

Project description:Study of BLaER1 cell line epigenetic changes induced throughout transdifferentiation. The Illumina Infinium MethylationEPIC Beadchip was used to obtain genomewide methylation profiles of BLaER1 cells at 7 different times throughout transdifferentiation treatment (0h, 3h, 12h, 24h, 48h, 72h and 168h). As a reference, the parental RCH-ACV cell line at 168h of treatment and anonymous donor blood derived macrophages were also profiled.

2019-11-28 | GSE132845 | GEO

Epigenetic analysis of BlaER1 transdifferentiation

Project description:Epigenetic analysis of BlaER1 transdifferentiation

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Histone modifications along transdifferentiation from B cell to macrophage

Project description:Transdifferentiation of BLaER1 B cell into macrophages is an appropriate model to understand how chromatin behaves along a dynamic process. With this purpose, we have performed chromatin immunoprecipitation experiments of two histone modifications associated to active enhancer activity along 4 time points of BLaER1 transdifferentiation.

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CRISPR-Cas9 screening of lncRNAs and protein coding genes involved in the transdifferentiation from human pre-B cells into macrophages

Project description:BLaER1 cells are human leukemia pre-B cells able to transdifferentiate into functional and non-tumorigenic macrophages. With the goal of uncovering the genes involved in the transdifferentiation process, we have designed a DECKO (Double Excision CRISPR Knockout) library to knockout lncRNAs and protein coding genes (pc-genes) overexpressed along the seven days the process lasts. We have seen that targeting pc-genes with two gRNAs synergistically enhances the efficiency of knock out, by inducing deletions and/or frameshifts that promote the expression of non-functional proteins. Thus, using the CRISPETa tool, we designed paired guide RNAs targeting either the region surrounding the Transcription Start Site of the 166 lncRNAs or the coding exons of the 874 pc candidate genes. Cas9-expressing BLaER1 cells were infected at low-multiplicity of infection with the combined library and induced transdifferentiation. Delayed and differentiated subpopulations of cells were isolated by Fluorescence-Activated Cell Sorting at 3 days and 6 days after induction, and pgRNAs were sequenced in an Illumina HiSeq2500 instrument. The sequencing reads were mapped and quantified to uncover the enriched pgRNAs found in each subpopulation. Among all genes targeted in the library, we identified twenty pc-genes and six lncRNAs as strong candidates to be involved in the process, as the pgRNAs targeting their loci were enriched in the delayed population compared to the differentiated one, either at 3 days or at 6 days after transdifferentiation induction. From these, we selected two pc-genes and two lncRNAs for deeper characterization.

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Project description:Exogenous overexpression of CEBPA transcription factor induces transdifferentiation from pro B cells into functional macrophages. Here we report the CEBPA binding ChIP-Seq data at 12 hours time point after induction of transdifferentiation in human BLaER1 cells (Rapino et al. 2013).

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Expression data from C/EBP alpha induced transdifferentiation of pre-B cells into macrophages

Project description:Earlier work has shown that pre-B cells can be converted into macrophages by the transcription factor C/EBP? at very high frequencies. Using this system we have now performed a systematic analysis of the question whether during transdifferentiation the cells transiently reactivate progenitor restricted genes or even retrodifferentiate. A transcriptome analysis of transdifferentiating cells showed that most genes are continuously up or downregulated, acquiring a macrophage phenotype within 5 days. In addition, we observed the transient reactivation of a subset of immature myeloid markers, as well as low levels of the progenitor markers Kit and Flt3 and a few lineage inappropriate genes. However, we were unable to observe the re-expression of cell surface marker combinations that characterize hematopoietic stem and progenitor cells (HSPCs), including c-Kit and Flt3. This was the case even when C/EBPalpha was activated in pre-B cells under culture conditions that favor HSPC growth or when the transcription factor was activated in a time limited fashion. Together, our findings are consistent with the notion that the conversion from pre-B cells to macrophages is mostly direct and does not involve overt retrodifferentiation. Our microarray data indicate that most expression changes are direct, and that transdifferentiation does not involve retrodifferentiation. Our data also show that there is a low level transient activation of selected progenitor genes, as well as myeloid precursor genes. Primary mouse pre-B cells were infected with an inducible form of C/EBPa and cells induced to transdifferentiate with beta Estradiol (b-Est) harvested at different time points to analyze expression profiles, using Affymetrix 430.2 arrays.

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