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108 results for “FOXA2;”
Aberrant development of pancreatic beta cells derived from human iPSCs with FOXA2 deficiency
<p><strong>Project manager(s)</strong><strong>: </strong>Essam M. Abdelalim</p> <p>Induced pluripotent stem cells (iPSCs) were generated from a patient with a heterozygous deletion of the short arm of chromosome 20 at bands p11.22 to p11.21 (~969 kb deletion), which contains only one gene, <em>FOXA2 </em>(<em>FOXA2<sup>+/-</sup></em>iPSCs) as well as healthy controls (Ctr1 iPSCs and Ctr2 iPSCs). <em>FOXA2<sup>+/-</sup></em>iPSCs were differentiated into different stages of beta cell development to understand the role of FOXA2 during pancreatic beta cell development as described in the article entitled "<strong>Aberrant development of pancreatic beta cells derived from human iPSCs with <em>FOXA2</em> deficiency" by Elsayed et al</strong>. The dataset represents RNA-seq data generated from pancreatic progenitors (PP2) and endocrine progenitors (EPs) derived from Ctr1 iPSCs, Ctr2 iPSCs, and three clones of <em>FOXA2<sup>+/-</sup></em>iPSCs. </p> <p>The file name is: Sample name _overall sample number_read direction_001 where:</p> <p>- PP2-Ctr 1: pancreatic progenitors (PP2) derived from Ctr1 iPSCs (healthy control 1)</p> <p>- PP2-Ctr 2: pancreatic progenitors (PP2) derived from Ctr2 iPSCs (healthy control 2)</p> <p>- PP2-FOX1, PP2-FOX2, and PP2-FOX3: pancreatic progenitors (PP2) derived from three different clones of patient-derived <em>FOXA2<sup>+/-</sup></em>iPSCs.</p> <p>- EP-Ctr1: endocrine progenitors (Eps) derived from Ctr1 iPSCs (healthy control 1)</p> <p>- EP-Ctr2: endocrine progenitors (Eps) derived from Ctr2 iPSCs (healthy control 2)</p> <p>- EP-FOX R1, EP-FOX R2, and EP-FOX R3: endocrine progenitors (EPs) derived from three different clones of patient-derived <em>FOXA2<sup>+/-</sup></em>iPSCs.</p> <p>- The RNA-Seq data were generated from two Ctr-iPSC lines and three FOXA2<sup>+/-</sup>iPSC lines.</p> <p>- Read direction: R1 (Forward), R2 (Reverse).</p>
Processed data for FOXA2 analysis in TCGA KIRP and KIRC patients
<pre># Data and code to test whether FOXA2 is changed in KIRP patients with low FH ## Code https://github.com/ArianeMora/foxa2_kirp_kirc ## Datasets RNA count data were downloaded from TCGA (https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga) using scidat (https://github.com/ArianeMora/scidat) for patients with kidney cancers (rna_df.csv). ## Processing The kidney cancer patient count data were split into KIRC and KIRP, and only the tumour data was used for this analysis, see notebook FOXA2.ipynb in the code folder. Samples were split by their expression of FH in their tumour samples, with several annotations used to separate patients for completeness: 1. Low-High: Comparing the bottom 25% (< Q1) of patients by FH vs “high” FH (i.e. top 25%, > Q3): p.adj 0.00004 2. Low-Normal: Comparing the bottom 25% of patients by FH to the patients with “normal” range FH (between Q1 and Q3): p.adj 0.053 3. Outlier-High: Comparing outlier FH to “high” (i.e. top 25%): p.adj 0.067 4. Outlier-Normal: Comparing the outlier FH (Q1 – 1.5*IQR) to all “normal” FH patients: p.adj 0.169 We did the same for KIRC patients – we don’t see FOXA2 as expected 1. Comparing the bottom 25% of patients by FH vs the top 25% of patients with FH: 0.14 2. Comparing the bottom 25% of patients by FH to the patients with “normal” range FH: 0.25 3. Comparing the outlier FH to all “normal” FH patients: 0.31 4. Comparing outlier FH to “high” (i.e. top 25%): 0.32 Each of these groups were used to also perform DE analysis between the two groups, see respective RMD files in code for details. ### References If you use this work please cite TCGA: ``` Creighton, C. J., Morgan, M., Gunaratne, P. H., Wheeler, D. A., Gibbs, R. A., Gordon Robertson, A., Chu, A., Beroukhim, R., Cibulskis, K., Signoretti, S., Vandin Hsin-Ta Wu, F., Raphael, B. J., Verhaak, R. G. W., Tamboli, P., Torres-Garcia, W., Akbani, R., Weinstein, J. N., Reuter, V., Hsieh, J. J., … University of North Carolina at Chapel Hill. (2013). Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature, 499(7456), Article 7456. https://doi.org/10.1038/nature12222 ``` </pre>
Data from: Forkhead box a2 (FOXA2) impacts uterine decidualization and fetoplacental development
<p class="MsoNoSpacing">Glands of the uterus are essential for the establishment of pregnancy in mice and likely humans. Forkhead box a2 (FOXA2) is a transcription factor expressed specifically in the glands of the uterus and a critical regulator of uterine gland differentiation, development and function. Mice with a conditional deletion of FOXA2 in the adult uterus, created using the lactotransferrin iCre (Ltf-iCre) model, have a morphologically normal uterus with glands, but lack a considerable number of FOXA2-dependent GE-expressed genes. Adult FOXA2 conditional knockout (cKO; Ltf-iCre:Foxa2 flox) mice are infertile due to defective embryo implantation arising from a lack of leukemia inhibitory factor (LIF), a critical implantation factor of uterine gland origin. Intraperitoneal injections of LIF can initiate embryo implantation in the uterus of adult FOXA2 cKO mice with pregnancies maintained to term. Here, we tested the hypothesis that FOXA2-regulated genes in the uterine glands impact development of the decidua, placenta and fetus using a littermate study design. On gestational day (GD) 8.5, the anti-mesometrial and mesometrial decidua transcriptome was noticeably altered in FOXA2 cKO mice. Viable fetuses were reduced in FOXA2 cKO mice on GDs 12.5 and 17.5. Sex-dependent differences in fetal weight, placenta histoarchitecture, and the placenta and metrial gland transcriptome were observed between control and FOXA2 cKO mice. The transcriptome of the placenta with a female fetus was considerably more altered than the placenta with a male fetus in FOXA2 cKO dams. These studies reveal a previously unrecognized biological role for FOXA2 and uterine glands on fetoplacental development that exhibits sexual dimorphism. Thus, uterine glands and, by inference, their products program fetoplacental development with potential sexually dimorphic impacts on offspring health into adulthood.</p>
Data from: Forkhead box a2 (FOXA2) impacts uterine decidualization and fetoplacental development
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Chromatin-immunoprecipitation followed by sequencing (ChIPseq) of SOX17 and FOXA2 in yolk-sac tumor cell lines
GEO Series GSE276475. Homo sapiens. 16 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Transcriptomic Analysis of Wild Type and FOXA2-/- ES-derived Pancreatic Progenitors
GEO Series GSE114099. Homo sapiens. 30 samples. Type: Expression profiling by high throughput sequencing.
Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2
GEO Series GSE116262. Mus musculus. 94 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing.
Siah2-dependent concerted activity of HIF and FoxA2 regulates formation of neuroendocrine prostate tumors
GEO Series GSE18478. Mus musculus. 12 samples. Type: Expression profiling by array.
Analysis of FoxA2 occupancy in mouse liver with endoderm ChIP-chip array
GEO Series GSE23551. Mus musculus. 3 samples. Type: Genome binding/occupancy profiling by genome tiling array.
Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2 [RNA-seq]
GEO Series GSE116259. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Cell differentiation grade determines distinct FOXA2 contributions to the cis-regulatory networks of pancreatic cancer cells [RNA-seq]
GEO Series GSE119931. Homo sapiens. 18 samples. Type: Expression profiling by high throughput sequencing.
[E-MTAB-115] ChIP-seq for FOXA2 HNF4a and NRF2 / GABP in HepG2
GEO Series GSE25694. Homo sapiens. 11 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Genome-wide maps of Foxa2 binding sites in mouse embryonic stem cell-derived definitive endoderm cells
GEO Series GSE40423. Mus musculus. 1 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Insm1 cooperates with Neurod1 and Foxa2 to maintain mature pancreatic β-cell function (Insm1, Neurod1 and Foxa2 ChipSeq data from pancreatic beta cell)
GEO Series GSE54046. Mus musculus. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
MicroRNA-590-3p promotes ovarian cancer growth and metastasis via a novel FOXA2-Versican pathway
GEO Series GSE113440. Homo sapiens. 6 samples. Type: Expression profiling by array.
The pioneer transcription factors Foxa1 and Foxa2 regulate alternative RNA splicing during positive selection in the thymus
GEO Series GSE169602. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
FOXA2 regulates a network of genes involved in critical functions of intestinal epithelia
GEO Series GSE66218. Homo sapiens. 3 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
FoxA1 and FoxA2 are required for gastric differentiation in NKX2-1-negative lung adenocarcinoma [single cell analysis]
GEO Series GSE115900. Mus musculus. 134 samples. Type: Expression profiling by high throughput sequencing.
Uncovering the role of FOXA2 in the development of human serotonin neurons [scRNA-seq]
GEO Series GSE232698. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
Uncovering the role of FOXA2 in the development of human serotonin neurons
GEO Series GSE232830. Homo sapiens. 14 samples. Type: Expression profiling by high throughput sequencing.
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