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ABSTRACT: FAW RNA seq control & EB treated

PROVIDER: PRJNA972552 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24580045_1.fastq.gz	Fastqsanger.gz
	SRR24580045_2.fastq.gz	Fastqsanger.gz
	SRR24580046_1.fastq.gz	Fastqsanger.gz
	SRR24580046_2.fastq.gz	Fastqsanger.gz

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Impact of maternal diet supplemented with selenium (Se) and vitamin B6 during pregnancy on gene expression of porcine expanded blastocysts (EB)

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Comparison of the transcription (coding and lncRNAs) of in vitro cultured bovine SAM-treated blastocysts and non-treated blastocysts

Project description:Transcriptome (total RNA) profiling of bovine in vitro cultured expanded blastocysts (EB) comparing control non-treated expanded blastocysts with SAM-treated expanded blastocysts. S-Adenosyl methionine (SAM) is the global methyl donor providing methyl group for variety of biomolecules such as DNA , histone, RNA, lipids and etc.

2016-02-29 | GSE75430 | GEO

Impact of maternal diet supplemented with selenium (Se) and vitamin B6 during pregnancy on gene expression of porcine expanded blastocysts (EB)

Project description:Transcriptional profiling of porcine expanded blastocysts comparing control (EB obtained from 4 sows treated with basal diet) with either inorganic Se + B6 (EB obtained from 4 sows treated with basal diet plus inorganic Se and B6) or organic Se + B6 (EB obtained from 3 sows treated with basal diet plus organic Se and B6). Three-condition experiment, EB without and with maternal diet supplemented B6 plus either inorganic Se or organic Se. Four biological replicates for inorganic Se and three biological replicates and one technical replicate for organic Se. Pooled of four biological replicates for control group.

2013-09-28 | E-GEOD-51249 | biostudies-arrayexpress

Comparison of the DNA methylation of in vitro cultured bovine SAM-treated blastocysts and non-treated blastocysts

Project description:Epigenetics (DNA methylation) profiling of bovine in vitro cultured expanded blastocysts (EB) comparing control non-treated expanded blastocysts with SAM-treated expanded blastocysts. S-Adenosyl methionine (SAM) is the global methyl donor providing methyl

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Project description:ATAC-seq data from EB-HSPC after AM580 treatment compared to DMSO-treated EB

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Effects of BPA, BPF and BPS treatments on mESC EB-based global and neural differentiations.

Project description:Purpose: the goal of this study is to determine the changes in gene expression during EB differentiation after BPA, BPF and BPS treatments, as indications of potential developmental toxicity. Methods: Transcriptomics profiling for EB samples treated with 100 nM BPA, BPF, BPS or DMSO control at different time points were generated by RNA-seq, using a BGISEQ-500 platform. Reads were filtered and aligned to the reference genome with Bowtie2. Results: BPA, BPF and BPS disrupted many processes, during mESC global and neural differentiations, in very similar manners. In fact, analogous gene categories were differentially regulated by the three chemicals, at each time point, particularly the ones involved in cell-matrix and cell-cell adhesions, signal transduction pathways, and medical conditions such as cardiovascular diseases and cancer.

2019-09-30 | GSE120224 | GEO

Taf4 is required for preinitiation complex formation at genes associated with neuronal differentiation

Project description:Occupancies of promoters by TBP, PolII, TFIIB as well as chromatin marks H3K4Me3 and H3K27ac were compared in embryonic stem cells (ESC) and in embryoid bodies (EB) treated with retinoic acid (RA) derived from the WT and Taf4a-/- lineages. Reduced occupancies for these factors and decreased signals for H3K4Me3 and H3K27ac were observed for genes associated with neuronal differentiation in EB of Taf4a-/- line compared to EB of WT line.

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Targeted differentiation of regional ventral neuroprogenitors and related neuronal subtypes from human pluripotent stem cells

Project description:Purpose: To find the mechanism for the differences in cell fates between the EB (embryoid body) and AD (adherent) culture conditions Methods: hESCs were cultured in different methods, and RNA-seq were generated , in triplicate, using Illumina GAIIx. The sequence reads were analyzed with Weighted gene correlation network analysis (WGCNA) and Gene Ontology (GO) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: We totally found roughly 600 genes which were specifically enriched in both day 4 EB cells and day 4 EB cells treated with SB431542 and LDN193189. Meanwhile, there were around 1000 genes which showed significant higher expression in AD cells Conclusions: complex intracellular cell contexts and extracellular components work together and define the distinct differentiation potencies of the AD and EB cells upon SHH patterning.

2016-10-15 | GSE82052 | GEO

Lentiviral expression of wildtype LAMA3A restores cell adhesion in airway basal cells from children with epidermolysis bullosa

Project description:The hallmark of epidermolysis bullosa (EB) is the fragile attachment of epithelia to underlying tissues due to genetic variants in genes involved in cell adhesion. A variety of epithelial surfaces can be affected, and EB patients who develop airway involvement suffer from a high degree of morbidity and mortality from laryngotracheal stenosis. Here, we describe 15 EB patients that were treated in the Ear, Nose and Throat department of a tertiary pediatric hospital linked to the United Kingdom’s National EB unit between 1992 and 2023. Investigation of the underlying genotypic status revealed that variants in LAMA3 were common in EB patients managed with airway complications (9/14 patients where genotype was available). Since LAMA3 encodes a subunit of the laminin-332 heterotrimeric extracellular matrix protein complex and is expressed by airway basal epithelial stem cells, we investigated the possibility of correcting LAMA3 in EB patient basal cell cultures. Airway basal cell cultures initiated from EB patients with variants affecting LAMA3 demonstrated fragile adherence to culture flasks but were otherwise expanded similarly to non-EB patient cell cultures. For genetic modification, we generated a lentiviral vector containing LAMA3A under the control of a constitutively active promoter sequence. In vitro transduction of primary EB patient-derived basal cell cultures restored cell attachment to levels comparable to a healthy control donor culture. Transduced cells could be expanded extensively in cell culture, suggesting their potential as an airway cell therapy for EB. We anticipate that our proof-of-concept data will be a starting point for translational combined cell and gene therapy for this rare patient group.

2024-02-01 | GSE249910 | GEO

Scl specifies hemogenic endothelium and inhibits cardiogenesis via primed enhancers [ChIP-seq]

Project description:Scl/Tal1 confers hemogenic competence and prevents cardiomyogenesis in embryonic endothelium. Here we show that Scl both directly activates a broad gene regulatory network required for hematopoietic stem/progenitor cell (HS/PC) development, and represses transcriptional regulators required for cardiogenesis. Cardiac repression occurs during a short developmental window through Scl binding to distant cardiac enhancers that harbor H3K4me1 at this stage. Scl binding to hematopoietic regulators extends throughout HS/PC and erythroid development and spreads from distant enhancers to promoters. Surprisingly, Scl complex partners Gata 1 and 2 are dispensable for hematopoietic versus cardiac specification and Scl binding to the majority of its target genes. Nevertheless, Gata factors co-operate with Scl to activate selected transcription factors to facilitate HS/PC emergence from hemogenic endothelium. These results uncover a dual function for Scl in dictating hematopoietic versus cardiac fate choice and suggest a mechanism by which lineage-specific bHLH factors direct the divergence of competing fates. ChIP-seq with Scl, Hand1, Lsd1, Ezh2, H3K4me1 and H3K27ac in different cell types with mesodermal origin. Scl ChIP-seq in WT, SclKO, SclKO-iScl and Gata12KO mES cell derived day4 EB (embryoid body) Flk1+ mesodermal cells, SclKO-iScl ES cells and MEL cells; Hand1 ChIP-seq in WT mES cell derived day4 EB Flk1+ mesodermal cells; Lsd1 and Ezh2 ChIP-seq in WT and SclKO mES cell derived day4 EB Flk1+ mesodermal cells. ChIP-seq of histone modifications H3K4me1 and H3K27ac in WT, SclKO and Gata12KO mES cell derived day4 EB Flk1+ mesodermal cells, HPC7 hematopoietic progenitor cells and HL1 cardiomyogenic cells

2015-01-01 | E-GEOD-47082 | biostudies-arrayexpress

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