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ChIP-Seq on Cohesin mutant TF-1 Cell Line

ABSTRACT: Understanding the binding of GATA2, RUNX1 and SMC3 in RAD21 WT vs. mutant TF-1 Cells

ORGANISM(S): Homo sapiens

PROVIDER: GSE73207 | GEO | 2015/11/03

SECONDARY ACCESSION(S): PRJNA296372

REPOSITORIES: GEO

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ChIP-Seq on Cohesin mutant TF-1 Cell Line

Project description:Understanding the binding of GATA2, RUNX1 and SMC3 in RAD21 WT vs. mutant TF-1 Cells We examined GATA2, RUNX1 and SMC3 using ChIP-seq in TF-1 erythroleukemia cells that were transduced with an inducible vector expression WT or mutant (Q592*) RAD21 after 6 days of DOX induction

2015-11-03 | E-GEOD-73207 | biostudies-arrayexpress

Gene expression profiling from cohesin knockdown cells obtained grown in methylcellulose

Project description:We performed RNA-sequencing in c-Kit+ cells that were infected with retroviruses expressing shRNAs for Renilla, Rad21, Smc1a, Smc3 or Stag2. These cells were grown in methylcellulose (M3434) for either one passage (P1) or replated for five passages (P5). RNA-sequencing control (Ren) and cohesin (Rad21, Smc1a, Smc3 and Stag2) knockdown cells.

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ATAC-seq of mouse Embryonic Stem Cell (mESC) line-derived cells subjected or not to doxycycline (dox)-induced overexpression of transcription factors

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Expression data from zebrafish embryos homozygous mutant for the cohesin subunit Rad21

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RNA-seq of mouse Embryonic Stem Cell (mESC) line-derived cells subjected or not to doxycycline (dox)-induced overexpression of transcription factors (TFs)

Project description:The RNA-seq is one of three readouts of an experiment carried out to assess the ability of different combinations of hematopoietic transcription factors to elicit the transdifferentiation of a mESC-derived non-hematopoietic cell type (vascular smooth muscle cells) into hematopoietic precursors upon dox-induced overexpression. The assessed trascription factors are Tal1, Lyl1 and Lmo2 (i3TFs), Runx1, Cbfb, Gata2, Fli1, Erg (i5TFs) and Runx1, Cbfb, Gata2, Tal1, Fli1, Lyl1, Erg, Lmo2 (i8TFs). The constructs for TF expression were stably integrated into mESCs and their expression induced by treatment with dox. i: inducible.

2023-05-15 | E-MTAB-12957 | biostudies-arrayexpress

Transcription profiling of zebrafish embryos homozygous mutant for the cohesin subunit Rad21

Project description:Rad21 is a subunit of cohesin. The main function of cohesin is to hold replicated chromosomes together until cells divide, but it also plays a role in gene expression. To find out which genes might be regulated by cohesin, a study was conducted to look for global changes in gene expression in zebrafish embryos lacking cohesin component Rad21. The zebrafish Rad21 mutant used for expression analysis was rad21nz171, an allele isolated in a forward genetic screen for regulators of runx1. Experiment Overall Design: RNA from rad21nz171 mutant and wild type zebrafish embryos collected at 24 hours post-fertilization (h.p.f.) and 48 h.p.f. was hybridized to Affymetrix microarrays (Gene Chip zebrafish genome arrays cat. no. 900488). Four pools of 50 embryos for each genotype and time point were used as the RNA source, and RNA from each pool was hybridized independently such that the experiment had four biological replicates.

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Project description:Combinatorial transcription factor (TF) interactions control cellular phenotypes and therefore underpin stem cell formation, maintenance and differentiation. Here we report the genome-wide binding patterns and combinatorial interactions for 10 key regulators of blood stem/progenitor cells (Scl/Tal1, Lyl1, Lmo2, Gata2, Runx1, Meis1, Pu.1, Erg, Fli-1, Gfi1b) thus providing the most comprehensive TF dataset for any adult stem/progenitor cell type to date. Genome-wide computational analysis of complex binding patterns followed by functional validation revealed the following: First, a previously unrecognized combinatorial interaction between a heptad of TFs (Scl, Lyl1, Lmo2, Gata2, Runx1, Erg, Fli-1). Second, we implicate direct protein-protein interactions between four key regulators (Runx1, Gata2, Scl, Erg) in stabilising complex binding to DNA. Third, Runx1+/-::Gata2+/- compound heterozygous mice are not viable with severe haematopoietic defects at midgestation. Taken together, this study demonstrates the power of genome-wide analysis in generating novel functional insights into the transcriptional control of stem and progenitor cells. 10 Samples (9 Transcription Factors and 1 Histone Modification) and 1 Control (IgG). All from the same cell line, a haematopoietic progenitor cell line (HPC-7).

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Expression profiling in cohesin mutant MCF10A epithelial and CMK leukaemia cells

Project description:MCF10A cells were CRISPR-Cas9 edited to create heterozygous deletion in RAD21 and SMC3 subunits of cohesin. STAG2 is on the X chromosome, hence CRISPR-Cas9 editing resulted in complete loss of STAG2. Total RNA was sequenced from the MCF10A parental and cohesin mutant MCF10A lines. The acute megakaryoblastic leukaemia cell line CMK was CRISPR-Cas9 edited to cotain STAG2 R614* mutation. CRISPR-Cas9 edited STAG2 mutant line showed complete loss of STAG2. CMK parental and the STAG2 mutant line were treated with Wnt3a for 4 hours and total RNA was sequenced at in the control or non-treated (con) and following 4 hours of Wnt3a treatment (Wnt3a4hr).

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