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RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of human early hematopoietic differentiation after LGR4 depletion and R-spondin2 treatment

ABSTRACT: RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of human early hematopoietic differentiation after LGR4 depletion and R-spondin2 treatment

PROVIDER: PRJNA486173 | ENA |

REPOSITORIES: ENA

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RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of human early hematopoietic differentiation after LGR4 depletion and R-spondin2 treatment

Project description:Purpose: The goals of this study are to identify differential genes and signaling pathways after LGR4 depletion and R-spondin2 treatment through comparing thel transcriptome profilings in hESC samples collected from day2 of co-cutlure hematopoietic differentiation. Methods: mRNA profiles of hESC samples collected from day 2 of 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: Treatment of R-spondin2 promotes up-regulation of mesoderm associated genes and LGR4 depletion severely down-reguletes mesoderm associated genes.

2018-08-16 | GSE118596 | GEO

RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of human early hematopoietic differentiation

Project description:Purpose: The goals of this study are to identify key transcription factors governing differentiation through comparing thel transcriptome profilings in hESC samples collected from day 0 to day 4 after hematopoietic differentiation. Conclusions: 68 transcriptional factors were found up-regulated gradually and steadily during early hematopoietic differentiation of H1 hESCs. After 4 days of differentiation, the mRNA levels of all these factors increased by more than 10 folds.

2018-01-31 | GSE92241 | GEO

RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of human ESCs early hematopoietic differentiation

Project description:RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of human ESCs early hematopoietic differentiation

| PRJNA510639 | ENA

RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of human ESCs early hematopoietic differentiation

Project description:Purpose:hESCs hematopoietic differentiation recapitulates embryonic hematopoiesis in vivo and occurs through three main stages: mesoderm commitment, hemogenic endothelium (HE) formation and hematopoietic specification. The goal of this study are to increase the understanding of hESCs hematopoietic differentiation process and its regulatory mechanism. Methods: hESC samples were collected through flow cytometry sorting.mRNA profiles of this samples 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: Compared with other three populations, 57 cell surface markers were highly enriched in CD31+CD34+ endothelial cells.

2018-12-19 | GSE124062 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Human Pluripotent Stem Cell-Derived Hematopoietic Cell Transcriptomes

Project description:Next-generation sequencing (NGS) has significantly advanced the elucidation of developmental signaling mechanisms that are important for different cell lineage formation from human pluripotent stem cells (hPSCs). We report here the application of RNA-sequencing technology for transcriptome profile of hPSC-derived hematopoietic cells, and compare to those of other cell lineages including hPSCs, mesoderm, primary aorta-gonad-mesonephros (AGM) cells and cord blood hematopoietic stem cells (HSCs). IIIumina HiSeq 2X150 bp sequencing was performed on three hematopoietic cell samples from three hPSC lines by GENEWIZ. The resulting sequence reads (about 34 million reads per sample) were mapped to human genome (hg19) using HISAT, and the RefSeq transcript levels (RPKMs) were quantified using the python script rpkmforgenes.py. Our RNA-seq data confirmed the stable expression of key hematopoietic cell markers including CD45, RUNX1, CD34 and HOXA clusters, and the gene set enrichment analysis (GSEA) showed enrichment in “aorta development”, “cell migration”, “hematopoietic stem cell proliferation”, “Notch signaling regulation”, et al. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to hematopoietic function. This study presented a detailed analysis of hematopoietic transcriptomes generated by RNA-seq technology, providing insight into the mechanisms underlying the differentiation of hPSCs into hematopoietic cells.

2022-05-13 | GSE155196 | GEO

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

Project description:Purpose: The goals of this study are to verify SNAI1 deletion is suffice to downregulate other MAGs during human early hematopoietic differentiation through comparing the transcriptome profilings in WT samples and SNAI1-knockout samples 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: Knockout of SNAI1 indeed suppresses the expression of other MAGs

2019-07-26 | GSE134911 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Human Pluripotent Stem Cell-Derived Hematopoietic Cell Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Human Pluripotent Stem Cell-Derived Hematopoietic Cell Transcriptomes

| PRJNA648952 | ENA

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 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 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

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