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RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of H1 derived cells with or without SB431542 treatment at Day8 after human early hematopoietic differentiation .

ABSTRACT: RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of H1 derived cells with or without SB431542 treatment at Day8 after human early hematopoietic differentiation .

PROVIDER: PRJNA556723 | ENA |

REPOSITORIES: ENA

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RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of H1 derived cells with or without SB431542 treatment at Day8 after human early hematopoietic differentiation .

Project description:Purpose: The goals of this study are to verify the inhibition of TGFb signaling is suffice to surpress the expression of MAGs in H1 cells during human early hematopoietic differentiation through comparing the transcriptome profilings in WT samples and samples with SB431542 treatment collected at day 8 after hematopoietic differentiation. Methods: mRNA profiles of hESC samples collected at day 8 after hematopoiesis differentiation were generated by deep sequencing using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Conclusions: Inhibiting TGFb signaling is suffice to significantly surpressed the expression of MAGs.

2019-07-26 | GSE134908 | GEO

RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of H1, H1 derived APLNR+ cells, CD31+CD34+ cells and CD43+ cells during human early hematopoietic differentiation

Project description:Purpose: The goals of this study are to verify the dynamic changes of MAGs in H1 derived different population of cells during human early hematopoietic differentian. Methods: mRNA profiles of hESC samples collected from day 0 to day 8 after hematopoiesis differentiation were generated by deep sequencing using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Conclusions:MAGs showed convincingly dynamic expression during early hematopoietic differentiation of H1 cells

2019-07-26 | GSE134907 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of primary cultured astrocytes treated with SB431542, Ro5-3335 and HLM006474 inhibitors.

Project description:Purpose: The goals of this study are to investigate differential genes expression with RNA-seq in primary cultured astrocytes treated with the Tgf-beta1 receptor inhibitor SB431542, the Runx1 inhibitor Ro5-3335 and the E2f1 inhibitor HLM006474. Methods: Primary cultured astrocytes were isolated from either C57BL/6 wild-type neonatal mice. Total RNA was extracted from SB431542, Ro5-3335 and HLM006474-treated astrocytes with the RNeasy Plus Micro Kit (Qiagen; 74034). mRNA profiles were generated by deep sequencing using Illumina NovaSeq 6000. The sequence reads that passed quality filters were aligned to the mouse reference genome (GRCm38) using the STAR software package. Differential expression analysis were performed using the R package DESeq2. qPCR validation was performed using SYBR Green assays. Results: After quality control and data filtering, about 50 million raw reads per sample were obtained. We mapped sequence reads per sample to the mouse reference genome (GRCm38) and identified 35825 transcripts vehicle, SB431542, Ro5-3335 and HLM006474 group. Differentially expressed genes (DEGs) were analyzed with a fold change ≥1.5 and p value <0.05. A total of 748 DEGs were identified in SB431542 group with 347 upregulated genes and 401 downregulated genes. A total of 397 DEGs were identified in Ro5-3335 group with 82 upregulated genes and 315 downregulated genes. A total of 856 DEGs were identified in HLM006474 group with 216 upregulated genes and 640 downregulated genes. Hierarchical clustering heat map, pathway enrichment and analysis of DEGs were performed. Conclusions: Our RNA-seq dataset represents the differentially expressed genes in the C57BL/6 astrocytes treated with SB431542, Ro5-3335 and HLM006474-treated astrocytes.

2022-11-23 | GSE174523 | GEO

Histone H1 facilitates restoration of H3K27me3 during DNA replication by chromatin compaction

Project description:Here we adopt ChOR-seq (Chromatin Occupancy after Replication) to monitor the dynamic re-establishment of H3K27me3 on nascent DNA during DNA replication. We found that the linker histone H1 facilitates the rapid post-replication restoration of H3K27me3 on repressive genes, which is essential for maintaining gene silencing and cell identity during cell division. Interestingly, the restoration rate of H3K27me3 on nascent DNA is greatly compromised after depletion of H1c/d/e. Finally, our in vitro biochemical experiments demonstrate that H1 facilitates the propagation of H3K27me3 by PRC2 through compacting chromatin. Collectively, our results indicate that H1-mediated chromatin compaction facilitates the propagation and restoration of H3K27me3 after DNA replication, which is key to cell fate determination.

2022-05-01 | GSE192984 | GEO

RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of H1 and H1 after SNAI1 deletion at Day2 after human early hematopoietic differentiation .

Project description:RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of H1 and H1 after SNAI1 deletion at Day2 after human early hematopoietic differentiation .

| PRJNA556725 | ENA

RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of H1 derived cells with or without IWP2 treatment at Day2 after human early hematopoietic differentiation .

Project description:Purpose: The goals of this study are to verify the inhibition of Wnt signaling is suffice to surpress the expression of MAGs in H1 cells during human early hematopoietic differentiation through comparing the transcriptome profilings in WT samples and samples with IWP2 treatment collected at day 2 after hematopoietic differentiation. Methods: mRNA profiles of hESC samples collected at day 2 after hematopoiesis differentiation were generated by deep sequencing using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Conclusions: Inhibiting Wnt signaling is suffice to significantly surpressed the expression of MAGs.

2019-07-26 | GSE134910 | GEO

RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of H1 derived CD31+ cells and H1 after HAND1-overexpression derived CD31+ cells at Day8 after human early hematopoietic differentiation .

Project description:Purpose: The goals of this study are to verify HAND1 overexpression is suffice to upregulate other MAGs in H1 cells during human early hematopoietic differentiation through comparing the transcriptome profilings in WT samples and HAND1-overexpressed samples collected at day 8 after hematopoietic differentiation. Methods: mRNA profiles of hESC samples collected at day 8 after hematopoiesis differentiation were generated by deep sequencing using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Conclusions: HAND1 overexpression is suffice to upregulate other MAGs during early hematopoietic differentiation of H1 cells.

2019-07-26 | GSE134906 | GEO

RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of H1 derived cells and H1 after MSX2-knockout derived cells at Day8 after human early hematopoietic differentiation .

Project description:Purpose: The goals of this study are to verify MSX2 knock is suffice to promote hematopoiesis during human early hematopoietic differentiation through comparing the transcriptome profilings in WT samples and MSX2-knockout samples collected at day 8 after hematopoietic differentiation. Method: mRNA profiles of hESC samples collected at day 8 after hematopoiesis differentiation were generated by deep sequencing using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Conclusions: MSX2 knock is suffice to promote hematopoiesis during early hematopoietic differentiation of H1 cells.

2019-08-01 | GSE135171 | GEO

RNA Sequencing Facilitates Quantitative Analysis of Wild Type and MEIS1 deleted H1 drived cells at day3 of hematopoietic differentiation

Project description:Purpose: The goals of this study are to investigate the molecular mechanism by which MEIS1 controls HEP specification through compareing the mRNA profiling of Wild Type and MEIS1 deleted H1 drived cells at day3 of hematopoietic differentiation. Conclusions:a large number of genes were down-regulated in MEIS1-deleted H1 hESCs when compared with the wild-type cells. Among those, a number of mammalian hematopoiesis-associated genes such as FLI1, APLN, TAL1 and MYB were significantly down-regulated.

2018-01-31 | GSE92243 | GEO

RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of H1, H1 derived APLNR+ cells, CD31+CD34+ cells and CD43+ cells during human early hematopoietic differentiation

Project description:RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of H1, H1 derived APLNR+ cells, CD31+CD34+ cells and CD43+ cells during human early hematopoietic differentiation

| PRJNA556721 | ENA

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