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Assay for Transposase-Accessible Chromatin of ATRA treated and wild type HL-60 cell line [ATAC-seq]

ABSTRACT: These ATAC-seq data were generated to correlate with genomic interaction data in a related Hi-C analysis. Analysis of ATAC-seq data revealed series of overlapping or specific open chromatin peaks in ATRA treated and control cells. Those specific peaks showed fewer overlapping with gene promoters than the overlapping peaks. Key transcription factor for blood cell differentiation GATA2 was found only bind in control specific peaks.

ORGANISM(S): Homo sapiens

PROVIDER: GSE93993 | GEO | 2018/03/07

REPOSITORIES: GEO

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Genome-wide maps of chromatin state ATRA treated and control HL-60 cells [ChIP-seq]

Project description:These ChIP-seq data were generated to correlate with genomic interaction data in a related Hi-C analysis.The goal of ChIP-seq are to annotate active promoter and enhancer of ATRA treated and control HL-60 cells. After ATRA induction, H3K27ac peaks distal to gene promoters showed significant changes. Those changes were correlated with interaction intensity between promoters and enhancers.

2018-03-07 | GSE93994 | GEO

Human HL-60 Cells: all-trans retinoic acid (ATRA) vs. ATRA plus arsenic trioxide (ATO)

Project description:Transcriptional profiling of human leukemia　HL-60 cells comparing ATRA treated HL-60 cells with ATRA plus ATO. Goal was to determine the effects of ATO on ATRA induced differentiation of HL-60 cells.

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Human HL-60 Cells: all-trans retinoic acid (ATRA) vs. ATRA plus arsenic trioxide (ATO)

Project description:Transcriptional profiling of human leukemia?HL-60 cells comparing ATRA treated HL-60 cells with ATRA plus ATO. Goal was to determine the effects of ATO on ATRA induced differentiation of HL-60 cells. Two-condition experiment, ATRA vs. ATRA plus ATO treated HL-60 cells.

2015-03-31 | E-GEOD-67420 | biostudies-arrayexpress

Expression Profiling of HL-60 Cells Stimulated by ATRA and DMSO

Project description:Stimulation of HL60 progenitor cells with either DMSO (1.25% v/v) or atRA (10E-07M) resulted in their differentiation into neutrophils within six days. Gene expression profiles across 12 600 genes were measured for the differentiation processes induced by DMSO and atRA at 0, 2, 4, 8, 12, and 18 h and daily thereafter until day 7 using oligonucleotide DNA microarrays. Keywords: time course, differentiation, cell fate transitions

2009-01-22 | GSE14500 | GEO

Transcription profiling of human HL-60 Cells Stimulated by ATRA and DMSO

Project description:Stimulation of HL60 progenitor cells with either DMSO (1.25% v/v) or atRA (10E-07M) resulted in their differentiation into neutrophils within six days. Gene expression profiles across 12 600 genes were measured for the differentiation processes induced by DMSO and atRA at 0, 2, 4, 8, 12, and 18 h and daily thereafter until day 7 using oligonucleotide DNA microarrays. Experiment Overall Design: The experiment consists of 24 Affymetrix hgu95av2 chips. 12 chips were used for the ATRA-stimulated time course, 12 chips were used for the DMSO-stimulated time course.

2009-01-30 | E-GEOD-14500 | biostudies-arrayexpress

The Study of ATRA-Induced Differentiation of the HL-60 Cell Line

Project description:Shotgun mass-spectrometric experiment was performed with HL-60 cells induced to differentiation at 0, 3, 24, 48 and 96h after ATRA treatment. Obtained data has been used for label-free quantification by SPIRE platform based on spectral count. Results on proteome profiling were used for up-stream regulator search in geneXplain platform (http://genexplain.com/).

2021-09-07 | PXD006768 | Pride

The epigenetic pattern and genome-wide CTCF occupancy in HL-60 cells treated with ATRA

Project description:10^7 HL-60 cells were treated with 10 uM ATRA for two and five days. 10% whole cell lysates were saved as input after genomic DNA was broken into 200-500 bp by sonication. 1 μg IP grade antibodies of CTCF, H3K4me3 or H3K27me3 (CST, Boston, USA) were incubated with the rest of the lysate overnight, followed by 2 h protein-A beads incubation at 4 °C for target protein pull down. The CTCF enriched or H3K4/27me3 modified DNA or input DNA were repaired to 3’-dA overhang and added the ligated adapter. The DNA library was eliminated the unligated adapters and selected the appropriate size for sequence using an Illumina X Ten platform. The raw sequence reads of input and IP were trimmed adaptors and filter out low quality reads using Cutadapt (v1.9.1) and Trimmomatic (v0.35), and checked the quality of clean reads using Fastqc. Next, clean reads were mapped to the human genome (assembly hg38) using the Bowtie 2 (v2.2.6) algorithm. The process of peak calling (p<0.01) were performed by MACS 2 (v2.1.1) and analyzed the different binding domains based on FDR value less than 0.05 and annotated by DiffBind. De novo motif were analyzed using the R language and MEME. The peaks on certain genomic loci were visualized by Integrative Genomics Viewer (IGV). Gene ontology (GO) Analysis was used to interpret the biological function of the genes associated with differential peaks.

2020-05-07 | E-MTAB-8558 | biostudies-arrayexpress

Differential Gene Expression between ATRA treated and control HL-60 Cells [RNA-seq]

Project description:These RNA-seq data were generated to correlate with genomic interaction data in a related Hi-C analysis. Analysis revealed differential expressed genes in ATRA treated and control HL-60 cells. Changes of gene expression with topological associated domains (TADs) were showd to be correlated with chromatin structure alteration

2018-03-07 | GSE93996 | GEO

Gene Expression-Based High Throughput Screening: HL-60 Cells Treated with ATRA and PMA

Project description:We developed a general approach to small molecule library screening called GE-HTS (Gene Expression-Based High Throughput Screening) in which a gene expression signature is used as a surrogate for cellular states and applied it to the identification of compounds inducing the differentiation of acute myeloid leukemia cells. In screening 1,739 compounds, we identified 8 that reliably induced the differentiation signature, and furthermore yielded functional evidence of bona fide differentiation. This data set contains HL-60 cells treated in a time course, in replicate, with 1 uM all trans retinoic acid (ATRA) and 10 nM phorbol 12-myristate 13-acetate (PMA). Also included are untreated HL-60 controls. This data set was used to select marker genes that distinguish the undifferentiated from the PMA or ATRA differentiated states. Keywords = AML Keywords = leukemia Keywords = HL-60 Keywords = chemical genomics Keywords: repeat sample

2004-01-30 | GSE985 | GEO

RNA seq of HL-60 cells in untreated, ATRA (All- trans retinoic acid) and Vitamin D3 treated conditions

Project description:The leukemic cell line HL-60 is widely used to study normal and aberrant myelopoiesis. HL-60 cells can be treated with ATRA (all-trans retinoic acid) and Vit-D3 (1,25-Dihydroxyvitamin D3, calcitriol) to differentiate into granulocytes and monocytes respectively. Induced myeloid differentiation helps us to understand the molecular basis of myeloid differentiation. To understand the genome-wide gene expression changes associated with HL-60 cells upon myeloid differentiation, RNA-sequencing was carried out. We subjected the HL-60 cells with 10 µM ATRA and 50 nM Vit-D3 for 72 hours. Post induction, the uninduced and induced cells were sorted based on CD11b and CD14 markers. The uninduced cells were negative for both the markers while ATRA and Vit D3 inductions were highly positive for CD11b-FITC and CD14-APC-H7 markers respectively. Two biological replicates were used for this experiment. Sorted cells were collected for RNA extraction using RNAeasy Kit from Qiagen and RNA quality was assessed using Bioanalyzer. High quality RNA with RIN values greater than 8, were used to generate library using TrueSeq stranded library preparation kit from Illumina following manufacturer’s instructions. Finally, barcoded libraries were pooled, and a final concentration of 10 nM was loaded in HiSeq 2500 Illumina platform and paired-end sequencing for 2*126 cycles were carried out.

2023-01-25 | E-MTAB-12267 | biostudies-arrayexpress

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