RNA-seq of hESCs undergoing primed to naive-like resetting via exogenous KLF17 overexpression
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 4000
ORGANISM(S): Homo sapiens
SUBMITTER: Rebecca Lea
PROVIDER: E-MTAB-10915 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Bulk RNA-seq of H9 human embryonic stem cells engineered to express a Dox-inducible KLF17_HA transgene. Uninduced (UI) and induced (+Dox) samples were collected each day between Day 0 (pre-induction) and Day 5 (post-Dox induction for +Dox or standard growth conditions for UI). Cells were continually cultured in conventional mTeSR1 hESC medium (StemCell Tech).
2021-10-02 | E-MTAB-10958 | biostudies-arrayexpress
Project description:Human preimplantation embryo development involves complex dynamic cellular and molecular events that lead to the establishment of the three lineages of the blastocyst â the trophectoderm, primitive endoderm and epiblast. Owing to limited resources of biological specimens, our understanding of how the earliest lineage commitments are regulated is limited. Here, we examined role for MCRS1, TET1, and THAP11 in inducing naive pluripotency in human embryonic stem cells in vitro. Human embryonic stem cells (H9) were nucleofected with piggybac constructs that encode for three genes (MCRS1, THAP11, TET1) followed by neomycin selection for 2 weeks to ensure stable integration. Overexpression of genes can be induced by doxycycline (dox) administration to the culture medium. Prior to dox treatment cells were cultured in conventional feeder-free conditions and then transferred to a feeder layer. Culture medium was switched from mTeSR to W8. Administration of dox and media change into 2i/LIF (2 inhibitors against MEK and GSK3 pathway + leukemia inhibitory factor) induces the overexpression of piggybac constructs and over time transitions primed pluripotent hESCs into a naive pluripotent state. Both pluripotent states were examined with microarrays in three biological replicates for each condition. MCRS1 = microspherule protein 1; TET1 = tet methylcytosine dioxygenase 1; THAP11 = THAP domain containing 11
2016-08-31 | E-MTAB-4567 | biostudies-arrayexpress
Project description:Purpose: Aim of the study is to identify functional differences between the P1 and P2-HNF4α isoforms. To do this, we generated Tet-On inducible lines that express either the human (P1) HNF4α2 or (P2) HNF4α8 under control of DOX in the HCT116 human colon cancer cells. Methods: HNF4α2 and Parental lines were induced with 0.3 μg/mL DOX, while HNF4α8 line was induced with either 0.1 or 0.3 μg/mL DOX for 24 hours. Samples were generated by deep sequencing, using the Illumina TruSeq RNA. Result: There were common and unique dysregulated genes identified in the HNF4α2 and HNF4α8 lines (+DOX); more upregulated genes than downregulated genes in both the lines. Conclusion: The functional difference between HNF4α2 and HNF4α8 is that the latter tends to upregulate genes involved in proliferation and anti-apoptosis while HNF4α2 upregulates genes involved in growth suppression and cell death. Tet-On inducible HCT116 cell (Parental, HNF4α2, and HNF4α8) lines, treated with (0.0, 0.1, or 0.3 μg/mL) DOX for 24 hours, were 50bp pair-ended sequenced in triplicate using Illumina TruSeq RNA Sample Prep v2 Kit.
2015-08-28 | E-GEOD-62889 | biostudies-arrayexpress
Project description:The motor neuron (MN)–hexamer complex consisting of LIM homeobox 3, Islet-1, and nuclear LIM interactor is a key determinant of motor neuron specification and differentiation. To gain insights into the transcriptional network in motor neuron development, we performed a genome-wide ChIP-sequencing analysis and found that the MN–hexamer directly regulates a wide array of motor neuron genes by binding to the HxRE (hexamer response element) shared among the target genes. Interestingly, STAT3-binding motif is highly enriched in the MN–hexamer–bound peaks in addition to the HxRE. We also found that a transcriptionally active form of STAT3 is expressed in embryonic motor neurons and that STAT3 associates with the MN–hexamer, enhancing the transcriptional activity of the MN–hexamer in an upstream signal-dependent manner. Correspondingly, STAT3 was needed for motor neuron differentiation in the developing spinal cord. Together, our studies uncover crucial gene regulatory mechanisms that couple MN–hexamer and STAT-activating extracellular signals to promote motor neuron differentiation in vertebrate spinal cord. To explain our experimental scheme briefly, we are interested in finding target sites for the dimer of transcription factors Isl1 and Lhx3. To mimic the biological activity of Isl1/Lhx3 dimer, we made Isl1-Lhx3 fusion and found that Isl1-Lhx3 has a potent biological activity in multiple systems (i.e. generation of ectopic motor neurons). Then we made ES cell line that induces Flag-tagged Isl1-Lhx3 expression upon Dox treatment. These *mouse* ES cells differentiate to motor neurons (iMN-ESCs) when treated with Dox following EB formation. To identify genomic binding sites of Isl1-Lhx3 (Flag-tagged), we performed ChIP with Flag antibody (pull down of Flag-Isl1-Lhx3) in ES cells treated with Dox. ChIP with Flag antibody in ES cells treated with vehicle (no Dox) was done as a negative control in parallel, and sequenced along with +Dox sample. We have done these experiments twice (two sets).
2013-09-19 | E-GEOD-50993 | biostudies-arrayexpress
Project description:Gene expression of T47D-MTVL human breast cancer cells expressing Dox-inducible shRNAs against histone H1.4 (sh120) or multiple H1 variants (sh225), or overexpressing WT or K26A mutant HA-tagged H1.4. T47D-MTVL, breast cancer cell line carrying one stably integrated copy of luciferase reporter gene driven by the MMTV promoter, is stably infected with an inducible system for the expression of shRNAs.Cells stably express RedFP and KRAB repressor fused to Tet regulator.Upon Dox treatment, cells express RedFP and the cloned shRNA. Stable breast cancer-derived cell lines expressing an shRNA against one of each of the histone H1 isoforms in response to doxycycline (Dox) were grown for six days in the presence or absence of Dox, in duplicate, and RNA extracted for microarray hybridization. Cell lines used: inducible shRNA against H1.4 or multiple H1 variants, and random shRNA-expression vector. Stable breast cancer-derived cell lines expressing the histone H1.4 isoform, WT or K26A, HA-tagged, in duplicate, and RNA extracted for microarray hybridization. Cell lines used: overexpressing H1.4 WT or K26A mutant.
2014-05-16 | E-GEOD-55786 | biostudies-arrayexpress
Project description:We previously demonstrated that hematopoietic stem cell (HSC)-like cells are robustly expanded from mouse embryonic stem (ES) cells by enforced expression of Lhx2, a LIM-homeobox domain (LIM-HD) transcription factor. Here we established an ES cell line which conditionally expressed Lhx2 by Tet-On system. The ES cells were differentiated into HSC-like cells by Lhx2 expression. Lhx2-regulated genes were identified by comparing the HSC-like cells with those cultured in the absence of Lhx2 expression. Mouse ES with inducible Lhx2 were differentiated on OP9 stromal cells into hematopoietic lineage. On day 5 of the differentiation induction,Lhx2 expression was started by the addition of doxycycline (dox) and the cells were cultured on OP9 stromal cells in the presence of IL-6 and SCF. On day 20, HSC-like cells were harvested and re-seeded onto OP9 stromal cells in the absence of Lhx2 expression by dox-removal for 3 days. these cells were compared with the original HSC-like cells.
2013-08-26 | E-GEOD-44778 | biostudies-arrayexpress
Project description:Prostate cancer is the most common, lethal malignancy in men. Although androgen withdrawal therapies are used to treat advanced disease, progression to a castration-resistant, end-stage is the usual outcome. In this study, the tested hypothesis was that the androgen receptor remains essential for the growth and viability of castration-resistant disease. Knocking down the androgen receptor in well-established tumors grown in castrated mice caused growth arrest, decreased serum PSA, and frequently regression and total eradication of tumors. Growth control of castration-resistant tumors appeared to be linked to the extent of androgen receptor knockdown, which triggers upregulation of many genes involved in apoptosis, cell cycle arrest, and inhibition of tumorigenesis and protein synthesis. Our findings provide proof of principle that in vivo knockdown of the androgen receptor is a viable therapeutic strategy to control and possibly eradicate prostate cancers that have progressed to the lethal castration-resistant state. C4-2 human prostate cancer cells stably expressing a tetracycline-inducible AR-targeted short hairpin RNA (shRNA) or scrambled shRNA were generated. These two cell lines were incubated in the absence of androgens with or without doxycycline hyclase (DOX). Comparison analysis of the gene expression profiles of C4-2 cells stably expressing AR shRNA + DOX and control cells (AR shRNA - DOX and scrambled shRNA ± DOX) was conducted to identify differentially regulated genes due to AR knockdown after normalization and data filtering. Genes were considered to be significantly different if the expression in the induced AR shRNA + DOX cells was at least 1.7-fold greater or 1.7-fold less than that seen in the control cells, with P< 0.05.
2010-06-23 | E-GEOD-13332 | biostudies-arrayexpress
Project description:The presence of extra centrosomes is a feature of human tumours. However, it is unclear what are the changes elicited by the presence of these abnormalities. To determine the changes in gene expression induced by centrosome amplification, human mammary epithelial cells, MCF10A, expressing a doxycycline inducible PLK4 cDNA were used. Centrosome amplification was induced for 48 hrs upon the addition of doxycyclin to the culture medium. RNA was purified from MCF10A cells without extra centrosomes (no dox) and with extra centrosomes (dox) and processed for microarray analysis.
2018-02-10 | E-MTAB-6415 | biostudies-arrayexpress
Project description:Purpose: Aim of the study is to determine how many of the dysregulated genes in the RNAseq are direct targets of (P1) HNF4α2 and (P2) HNF4α8 and examine HNF4α and TCF4 binding in vivo. We performed ChIPseq on TCF4 in the absense or presence of DOX in the Tet-On inducible HCT116 HNF4α2 and HNF4α8 lines, and ChIPseq for HNF4α (a445 Ab) in the presence of DOX. Methods: HNF4α2 and HNF4α8 lines were induced with 0.3 μg/mL DOX for 24 hours. Samples were generated by deep sequencing, using the NEXTflex ChIPseq. Result: There were more HNF4α2 peaks than HNF4α8 peaks, with some common peaks bound by HNF4α2 and HNF4α8. Binding patterns were observed between HNF4α and TCF4. Conclusion: HNF4α2 can displace TCF4 better than HNF4α8 on AP-1 bound sites. Tet-On inducible HCT116 cell (HNF4α2 and HNF4α8) lines, treated with (0.3 μg/mL) or without DOX for 24 hours, were 50bp single-end sequenced using Illumina-compatible-NEXTflex ChIP kit (Bioo Scientific).
2015-08-28 | E-GEOD-62890 | biostudies-arrayexpress
Project description:To understand the role of DPPA2 in epigenetic memory during X-Chromosome reactivation (XCR) we employed inducible Xist hybrid female embryonic stem cell line (TX1072, hybrid Bl6/Cast). Wild type or Dppa2 knockout TX1072 cells were cultured, in three or two independent biological replicates, respectively, in presence of DOX (1ug/ml) for 6 days to induce Xist overexpression and X-Chomosome inactivation (XCI) on the Bl6 allele. DOX was then washed out to silence Xist and XCR was followed in a time-series at 1, 3 or 7 days after DOX removal. Cell pellets were harvested at the following timepoints: -DOX, +DOX, 1d D-wo, 3d D-wo and 7d D-wo. RNA was extracted and 250 ng used for PolyA mRNA library preparation and Next generation sequencing.
2021-11-23 | E-MTAB-11183 | biostudies-arrayexpress