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Next Generation Sequencing Facilitates Quantitative Analysis of transcriptomes of human cord blood CD34+ cells treated with HDAC5 inhibitor

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of transcriptomes of human cord blood CD34+ cells treated with HDAC5 inhibitor

PROVIDER: PRJNA434440 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6743200.fastq.gz	Fastqsanger.gz
	SRR6743201.fastq.gz	Fastqsanger.gz
	SRR6743202.fastq.gz	Fastqsanger.gz
	SRR6743203.fastq.gz	Fastqsanger.gz
	SRR6743204.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing Facilitates Quantitative Analysis of transcriptomes of human cord blood CD34+ cells treated with HDAC5 inhibitor

Project description:We have used RNA-seq based transcriptome characterization to analyze differentiated gene expression in human cord blood CD34+ cells treated with vehicle control or HDAC5 inhibitor LMK235

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Project description:Global gene expressions of human cord blood-derived 18Lineage-negative (18Lin-)CD34+CD38-CD133+GPI-80+ cells (CD34+ HSCs), 18Lin-CD34-CD133+GPI-80+ cells (CD34- HSCs) and 18Lin-CD34+CD133- cells (non-HSCs) were analyzed. Results provide an insight into the molecular mechanisms underlying the self-renewal, maintenance and differentiation of human cord blood-derived CD34+/- HSCs.

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Transcription profiling of human AML1-ETO transduced cord blood cells, CD34 selected, compared to normal cord blood cells, CD34 selected

Project description:AML1-ETO expression in normal human umbilical cord blood CD34+ cells leads to long-term proliferation of an early self-renewing primitive progenitor cell with multilineage potential and stem cell ability, but these cells do not induce leukemia in immunodeficient mice. This comparative microarray study was initiated to determine the differences in the transcriptome of AML-ETO-expressing CD34+ cells after extended culture in vitro, using normal cord blood cells expanded for 6-8 weeks in vitro and subsequently purified for the CD34+ population as the control comparison. Experiment Overall Design: We have established a culture system whereby we retrovirally transduce human CD34+ cells, obtained from cord blood, with the leukemia fusion gene AML1-ETO. Cells expressing this fusion protein are able to proliferate long-term in vitro in a cytokine dependent manner. AML1-ETO-expressing cord blood cells have a large population of primitive self-renewing CD34+ cells with continued abnormal differentiation. We grow these cells in serum-free conditions using the BIT supplement from Stem Cell Technologies. For the current experiments we used cell cultures that had been proliferating in vitro for 8-12 weeks, in a cytokine cocktail of SCF, TPO, FLT3L, IL-6 all at 20 ng/mL and IL-3 at 10 ng/mL. Control cord blood samples that were CD34 purified were expanded for 5-8 weeks in the same culture media as used for AML1-ETO cells. All samples were magnetically selected for the CD34+ population, returned to culture, and one week later again selected for CD34+ cells and then lysed for RNA isolation.

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HDAC5-ChIP seq data in HDAC5-driven KRASG12D-independent PDAC cells

Project description:HDAC5 belongs to Class IIa histone deacetylases and forms corepressor complex with HDAC3 to suppess gene expression. To identify the target genes of HDAC5, we performed ChIP-seq analysis in FLAG-tagged HDAC5 PDAC escaper cells. HDAC5 binding chromatins were pulled down by HDAC5 antibody and FLAG antibody as replicates.

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Epigenetic and molecular signatures of cord blood CD34(+) cells treated with histone deacetylase inhibitors

Project description:Gene expression profiling of primary cord blood hematopoietic stem cell (day 0, CD34+ cells), enriched control (untreated), Scriptaid and Valproic acid expanded CD34+ cells after a week in culture. Cord blood CD34+ cells were processed individually and equal number of PC and reisolated CD34+ cells from 3-4 samples were pooled after expansion to avoid sample variations.

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ADGRG1/GPR56 knockdown in cord blood CD34+ cells

Project description:ADGRG1/GPR56 was knocked down by two different shRNAs in cord blood CD34+ cells via lentiviral transduction. GFP was used as marker indicating successful transduction.

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RNAseq data comparing HDAC5 eccaper PDAC cells with HDAC5 knockdown and scramble control

Project description:HDAC5 drives PDAC cells to bypass KRAS* dependency. To dissect the molecular mechanisms that regulated by overexpressed HDAC5 in escaper cells, we conducted RNA-seq analysis of HDAC5 escaper PDAC cells knocking down of HDAC5 or scramble shRNA control.

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