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Assay for transposase-accessible chromatin with sequencing (ATAC-seq) after various treatments in T47D cells

ABSTRACT: This experiment identifies the primary estrogen response genes in T47D cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE251793 | GEO | 2023/12/21

REPOSITORIES: GEO

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Nascent RNA sequencing (PRO-seq) after various treatments in T47D cells

Project description:This experiment identifies the primary estrogen response genes in T47D cells.

2023-12-21 | GSE251785 | GEO

Nascent RNA sequencing (PRO-seq) after estrogen treatment in T47D cells

Project description:This experiment identifies the primary estrogen response genes in T47D cells.

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ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing.

Project description:Spatial organization of the genome plays a central role in gene expression, DNA replication, and repair. But current epigenomic approaches largely map DNA regulatory elements outside of the native context of the nucleus. Here we report assay of transposase-accessible chromatin with visualization (ATAC-see), a transposase-mediated imaging technology that employs direct imaging of the accessible genome in situ, cell sorting, and deep sequencing to reveal the identity of the imaged elements. ATAC-see revealed the cell-type-specific spatial organization of the accessible genome and the coordinated process of neutrophil chromatin extrusion, termed NETosis. Integration of ATAC-see with flow cytometry enables automated quantitation and prospective cell isolation as a function of chromatin accessibility, and it reveals a cell-cycle dependence of chromatin accessibility that is especially dynamic in G1 phase. The integration of imaging and epigenomics provides a general and scalable approach for deciphering the spatiotemporal architecture of gene control.

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T47D shNT versus T47D shRON

Project description:T47D shNT versus T47D shRON

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Assay for Transposase Accessible Chromatin (ATAC)-sequencing of the AML cell line U937

Project description:All-trans retinoic acid (ATRA, RA) has powerful activity in APL; its efficacy in non-APL AML is still unclear, but may be boosted by epigenetic drugs such azanucleoside DNMT inhibitors (Blagitko-Dorfs et al. PLoS ONE 2013). In a randomized phase II study (DECIDER trial, NCT00867672) the addition of RA to decitabine (DAC) in newly diagnosed non-fit older AML patients resulted in a clinically meaningful extension of survival. We hypothesize that in vitro, the add-on of RA to DAC results in cooperative transcriptome and chromatin accessibility changes (possibly associated with demethylation), which may explain at least in part this clinical result.

2022-08-31 | GSE190878 | GEO

ER/PR RIME Experiments in MCF7 and T47D cell lines

Project description:Immuno-precipitation followed by MS was performed using the RIME protocol in this study. Estrogen Receptor (ER) and Progestorone Receptor (PR) were targetted using antibodies. The experiments were performed in a quantitative manner using SILAC labelling. Cells grown in complete serum (estrogenic) conditions were compared against an cells in similar complete media, however supplemented with Progesterone (PG) or R5020 for 4 hours. Experiments were performed in MCF7 and T47D cell lines

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Next Generation Sequencing Facilitates Quantitative Analysis of human breast cancer cell T47D and T47D-TR Transcriptomes

Project description:To gain new insight into the resistance to hormonal therapy in breast cancer, we generated a tamoxifen-resistant human breast cancer cell line T47D-TR by exposing estrogen-sensitive cell line T47D to increasing concentrations of 4-hydroxy tamoxifen (4-OHT) and identified its resistance with different ways. What we interested is the underlying mechanisms of breast cancer tamoxifen resistance which was not reported yet.Here, we detect the RNA sequence of both the two cell lines hoping to find some evidence.

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Protocol for assay of transposase accessible chromatin sequencing in non-model species.

Project description:The assay for transposase accessible chromatin (ATAC-seq) is a method for mapping genome-wide chromatin accessibility. Coupled with high-throughput sequencing, it enables integrative epigenomics analyses. ATAC-seq requires direct access to cell nuclei, a major challenge in non-model species such as small invertebrates, whose soft tissue is surrounded by a protective exoskeleton. Here, we present modifications of the ATAC-seq protocol for applications in small crustaceans, extending applications to non-model species. For complete information on the use and execution of this protocol, please refer to Buenrostro et al. (2013).

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Genomic binding profiles of ERa in MCF-7 and T47D control or enhancer588-targeted cells

Project description:Estrogen Receptor a (ERa) bindning to DNA was profiled by ChIP-seq in MCF-7 and T47D cells transduced with either control sgRNA, or sgRNA targeting a specific enhancer region (enhancer588). ERa in MCF-7 and T47D control or enhancer588-targeted cells

2015-12-14 | E-GEOD-75779 | biostudies-arrayexpress

Differential expression levels of mRNAs in tamoxifen-sensitive T47D versus tamoxifen-resistant T47D (T47DR) human breast cancer cells

Project description:Tamoxifen is the most widely used antiestrogen in patients with estrogen receptor (ER) positive breast cancer . However, less than half of patients benefit from tamoxifen treatment and 30-50% acquire resistance and the disease progresses. Resistance to tamoxifen is a serious problem in breast cancer therapy and major efforts are underway to find out underlying mechanisms. To find out the differential expression levels of mRNAs in tamoxifen-sensitive T47D versus tamoxifen-resistant T47D (T47DR) human breast cancer cells, T47DR (tamoxifen-resistant) cell line was established from T47D cells after the following continuous exposure to 1 μmol/L 4-Hydroxytamoxifen (H7904, Sigma, USA) for more than 6 months.Thousands of significantly different mRNA expression levels were found and analysed. Our study provides a reference data for the study of tamoxifen resistance .

2020-06-01 | GSE129544 | GEO

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