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TP53 promotes lineage commitment of human embryonic stem cells through ciliogenesis and sonic hedgehog signaling [RNA-Seq]

ABSTRACT: H9 WT ESCs or TP53 KO (Clone 1) ESCs were injected subcutaneously into mice for teratoma formation. 6-8 weeks later, teratomas were isolated and total RNA was purified. TruSeq library preparation kit from Illumina was used to make libraries for RNA-Seq. NGS sequencing on Illumina NextSeq 500 was performed and data was analyzed to determine changes in transcriptome between WT and TP53 KO teratoma cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE168678 | GEO | 2022/02/16

REPOSITORIES: GEO

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TP53 promotes lineage commitment of human embryonic stem cells through ciliogenesis and sonic hedgehog signaling [RNA-Seq 2]

Project description:NGS was used to analyze role of TP53 in differentiation of human embryonic stem cells. RNAseq and was done in WT and p53 KO embryonic stem cells (ESCs) and in in vitro differentiated Neural progenitor cells (NPCs).

2022-02-16 | GSE168752 | GEO

TP53 promotes lineage commitment of human embryonic stem cells through ciliogenesis and sonic hedgehog signaling [ChIP-seq]

Project description:NGS was used to analyze role of TP53 in differentiation of human embryonic stem cells. TP53, a transcription factor, binds DNA and regulates transcription of specific genes. Chipseq of TP53 was done on WT ESCs and NPCs to identify direct targets of TP53 during differentiation of hESCs into neuronal lineage.

2022-02-16 | GSE168584 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of TP53-WT and TP53-KO HCT116 cells transcriptomes [RNA-seq]

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare TP53-WT and TP53-KO HCT116 cells transcriptome profiling (RNA-seq) under 5-FU treatment condition and to evaluate the correlation between transcriptome profileing and chromatin accessibility under 5-FU treatment. Methods: HCT116 cell profiles of TP53-WT and TP53- KO were generated by deep sequencing, in duplicates, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform levels: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA). Conclusions: Our study represents the detailed analysis of TP53-WT and TP53-KO HCT116 cell transcriptomes under 5-FU treatment with different timepoint, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that RNA-seq offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a TP53-WT and TP53-KO cells with and without 5-FU treatment in different timepoint. We conclude that NGS based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

2021-02-10 | GSE157951 | GEO

Zfp296 knockout enhances chromatin accessibility and induces a unique state of pluripotency in embryonic stem cells [RNA-seq-2]

Project description:Zfp296-KO ESCs grew as flat colonies and could not form teratomas, but could contribute to germline-competent chimeric mice. To analyze the molecular mechanisms causing these unique phenotypes, we compared gene expression profiles among wild-type (WT), Zfp296-KO, and Zfp296-rescue ESCs by RNA-sequencing.

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Zfp296 knockout enhances chromatin accessibility and induces a unique state of pluripotency in embryonic stem cells [RNA-seq-1]

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Expression data from embryonic stem cells (ESCs) and ESC-like cells

Project description:The transplantation of ESCs into living recipients causes teratoma formation which accompanies with several biological reactions in both the transplanted cells and recipient. Co-injection of ESCs with somatic cells that influence donor-recipient homogeneity can affect transcriptional profile of transplanted ESCs. We investigated global gene expression of parental ESCs and ESC-like cells derived from teratomas which were formed by different injection conditions to find transcriptional differences according to donor-recipient homogeneity and somatic cell co-injection. Parental ESCs or teratoma-derived ESC-like cells from different treatments were retrieved for RNA extraction and hybridization on Affymetrix microarrays.

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Expression data from control (F/F) and Snai1 knockout (KO) embryoid body (EB) and teratoma ™

Project description:Snai1 is a master factor of epithelial to mesenchymal transitioin (EMT), however, its role in embryonic stem cell (ESC) differentiation and lineage commitment remains undefined. We used microarrays to compare the global programme of gene expression between control and Snai1 knockout ESCs-derived EB and teratoma. For EBs, control and Snai1 knockout ESCs were cultured as embryoid bodies in spotaneous differentiation media, RNA of 5 days EBs were collected for Affymetrix microarrays. For teratomas, control and Snai1 knockout ESCs were injected into nude mice to form teratomas. RNA of 6 weeks were collected for Affymetrix microarrays.

2013-12-10 | E-GEOD-53106 | biostudies-arrayexpress

TP53 promotes lineage commitment of human embryonic stem cells through ciliogenesis and sonic hedgehog signaling [CRISPR screen]

Project description:CRISPR-Cas9 screen was done to identify genes required for NPC differentiation. Sox1 is an established NPC marker. Human ESCs were infected with GecKO v2 library, selected with puromycin and then allowed to differentiate into Neural progenitor cells (NPC) using StemDiff monolayer protocol (Stem cell Technologies). Day 7 NPCs were collected and FACS sorted to obtain bottom 1% of Sox1 expressing cells. NGS was used to identify guide sequences in cell population and determine the genes required for Sox1 expression during NPC differentiation.

2022-02-16 | GSE168585 | GEO

Expression data from embryonic stem cells (ESCs) and ESC-like cells

2014-06-23 | GSE58725 | GEO

Effects on gene expression of RNA polymerase I inhibitor CX-5461 in control and TP53-knockout cell lines of multiple myeloma

Project description:Multiple myeloma cell lines MM1S and MOLP8 were modified by zinc finger nucleases targeting exon 7 of the TP53 DNA binding domain. Knockout (KO) clones were isolated by limiting dilution, identified by TP53 resequencing, and confirmed by Western blotting. KO and unmodified (WT) clones were then either treated with vehicle or 200 nM CX-5461 for 48 hours for gene expression profiling (GEP).

2019-10-01 | GSE73665 | GEO

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