Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chromatin accessibility profiling of the pig limbic and endocrine tissues

ABSTRACT: This experiment investigated chromatin accessibility of the pig limbic and endocrine tissues, which are important in stress response and hence the pig’s health and welfare and production. We carried out a total of 48 ATAC-seq profiles of the amygdala, hippocampus, thalamus, hypothalamus, pituitary gland, and adrenal gland obtained from 8 individual pigs. We compared the chromatin accessibility landscape across tissue-type, annotated differentially accessible genomic regions and functionally mapped them.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Sus scrofa

SUBMITTER: Nares Trakooljul

PROVIDER: E-MTAB-14923 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Chromatin accessibility profiling of the jejunum mucosa of two laying hen strains associated with low dietary Phosphorus

Project description:This study investigated changes of chromatin accessibility of the gut associated with the removal and reduction of Phosphorus (P) (0 and 1 g P/kg feed) during the transition to egg production at 19 and 24 weeks (before and after the onset of laying, respectively) of Lohmann Brown (LB) and Lohmann Selected Leghorn (LSL) chickens. The experiment is a 2x2x2 factorial design, encompassing two strains, age groups, and diets and including a total of 80 (LB and LSL) hens. Unfortunately, two outliers were excluded from the final analysis based on quality control of library preparation and sequencing.

2026-04-24 | E-MTAB-14836 | biostudies-arrayexpress

Transcriptomic profiling of the pig limbic and endocrine tissues

Project description:This study aims to investigate the transcriptomic profile of the pig limbic and endocrine tissues, which are important in stress response and hence the pig’s health and welfare and production. We performed a total of 48 RNA-seq of the amygdala, hippocampus, thalamus, hypothalamus, pituitary gland, and adrenal gland obtained from 8 individual pigs. We identified differentially expressed genes across tissue-types, co-expressed gene modules and their associations with specific tissue types by Weighted Gene Co-expression Network Analysis (WGCNA) and allele-specific expression (ASE) within and between tissues.

2025-07-30 | E-MTAB-14452 | biostudies-arrayexpress

Bulk ATAC-Sequencing of isolated spermatocytes from testis tissue from B6/CAST F1 hybrid mice

Project description:We performed profiling of allele-specific chromatin accessibility profiling in mouse spermatocytes. To this end, we isolated tetraploid spermatocytes using FACS-sorting from F1 crosses of the C57B6J and CAST/EiJ strains. We then performed ATAC-Seq (Corces et al. 2017) and analyzed allele-specific chromatin accessibility.

2023-12-01 | E-MTAB-12685 | biostudies-arrayexpress

Histone Reader BRWD1 Targets and Restricts Recombination to the Igk Locus

Project description:B lymphopoiesis requires that immunoglobulin genes be accessible to RAG1-RAG2 recombinase. However, the RAG proteins bind widely to open chromatin, which suggests that additional mechanisms must restrict RAG-mediated DNA cleavage. Here we show that developmental downregulation of interleukin 7 (IL-7)-receptor signaling in small pre-B cells induced expression of the bromodomain-family member BRWD1, which was recruited to a specific epigenetic landscape at Igk dictated by pre–BCR-dependent Erk activation. BRWD1 enhanced RAG recruitment, increased gene accessibility and positioned nucleosomes 5? to each J? recombination signal sequence. BRWD1 thus targets recombination to Igk and places recombination within the context of signaling cascades that control B cell development. Our findings represent a paradigm in which,at any particular antigen-receptor locus, specialized mechanisms enforce lineage- and stage-specific recombination. ChIP-seq for 1 transcription factor and 2 histone modifications in flow purified mouse small pre-B cells. ATAC-seq and RNA-seq in WT and Brwd-Mut mouse flow purified small pre-B cells.

2015-08-24 | E-GEOD-63302 | biostudies-arrayexpress

ATAC-seq of primary mammalian aortic endothelial cells before and after TNFα stimulation

Project description:To identify conserved TNFα-induced changes in chromatin-accessibility in mammals, we performed ATAC-seq in primary vascular endothelial cells (ECs) isolated from the aortas of human (HAEC), mouse (MAEC) and cow (BAEC), before and after TNFα. We overlay our data with multi-species NF-κB binding data and identify multiple modes of NF-κB-chromatin interactions that are conserved during mammalian TNFα response. Our cross-species approach identifies conserved changes in chromatin-accessibility at NF-κB binding sites that are disease-relevant and essential during mammalian acute inflammation.

2020-06-01 | E-MTAB-7878 | biostudies-arrayexpress

ATAC-seq of human ALK negative ALCL cell line (TLBR2) in parental and HELLS knockdown conditions

Project description:Characterization of chromatin accessibility in T-cell lymphoma. ATAC-seq experiments were performed in both control (CT) and HELLS knockdown (shHELLS) cells to evaluate changes in chromatin accessibility.

2025-11-02 | E-MTAB-13851 | biostudies-arrayexpress

ATAC-seq analysis of the day-night rhythm in chromatin accessibility in PCM1+ left ventricular cardiomyocyte nuclei

Project description:This study investigated differential chromatin accessibility at zeitgeber time (ZT) 0 denoting the start of the light/inactive period in mice compared to ZT12 (the start of the dark/active) period to obtain insights into diurnal changes in transcription factor binding and gene regulatory pathways in the mouse cardiomyocytes.

2024-02-29 | E-MTAB-13696 | biostudies-arrayexpress

Transcriptional dysregulation associated with chromatin accessibility of iPSC and hepatocytes derived from a Cornelia de Lange syndrome patient (ATAC-Seq - iPSCs [N])

Project description:Cornelia de Lange syndrome (CdLS) is a rare genetic disease associated with cohesinopathy. A novel iPSC line was generated from the CdLS patient carrying a heterozygous missense point-mutation of the NIPBL gene. iPSC lines prepared from the healthy parents and the mutation-corrected isogenic cell lines are used as the respective controls. Upon differentiation into hepatocytes, the patient-derived iPSC demonstrate the capacity to express hepatocyte-specific marker transcripts and the respective proteins, however, the efficiency of differentiation is significantly inferior to those of the respective controls, demonstrated by single-cell RNA sequencing and immune-fluorescent analyses. Global change of transcriptome in the patient-derived iPSC relative to the control cells is associated with altered chromatin accessibility, assessed by RNAseq combined with ATACseq analysis. Differentially down-regulated genes in the patient-derived iPSC, in particular, are those coding for proteins related to neural differentiation and transcription factors, while up-regulated genes contain some of antisense RNA coding genes, pseudo genes and long non-coding RNAs. Some of the differentially regulated genes are consistent with the altered chromatin accessibility and this observation is consistent during hepatocyte differentiation. Thus, the mutation in the NIPBL gene of the CdLS patient could be responsible for defects of differentiation primarily due to alteration of chromatin accessibility.

2023-11-01 | E-MTAB-13240 | biostudies-arrayexpress

ATAC-seq of RS4:11 cell line populations that are unedited (SPI1 +/+), mono (SPI1 +/-) and biallelicaly edited (SPI1 -/-)

Project description:The goal of the experiment was to understand the epigenetic effects of PU.1 haploinsufficiency on pro-B cells. The RS4:11 cell line was edited both mono and biallelicaly via electroporation of Cas9 and guides. Following editing, aliquots of unedited (SPI1 +/+), mono (SPI1 +/-) and biallellicaly edited (SPI1 -/-) cells were lysed before undergoing the transposition reaction. After transposition, the ATAC-seq libraries were purified and then amplified via PCR. Libraries were sequenced using the Illumina Novaseq platform.

2021-03-24 | E-MTAB-8676 | biostudies-arrayexpress

Transcriptional dysregulation associated with chromatin accessibility of iPSC and hepatocytes derived from a Cornelia de Lange syndrome patient (ATAC-Seq - D9)

2023-06-23 | E-MTAB-12684 | biostudies-arrayexpress