Primary monocyte to macrophage differentiation involves significant changes in chromosome conformation different from cultured THP-1 cells
Ontology highlight
ABSTRACT:
INSTRUMENT(S): HiSeq X Ten
ORGANISM(S): Homo sapiens
SUBMITTER: Zhang Zhipeng
PROVIDER: E-MTAB-8261 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Use human native monocyte and induce to macrophae by GM-CSF, reserach the chromatin conformation of these two cell types.
2021-02-23 | E-MTAB-8262 | biostudies-arrayexpress
Project description:We found the expression of SLC22A18 in short stature patients is lower than that in controls by qPCR. DNA methylation is one of the most possible reason to make the expression of SLC22A18 abnormal. So we quantified the promoter methylation levels of 3 patients and 3 healthy controls by deep sequencing.
2021-09-03 | E-MTAB-9579 | biostudies-arrayexpress
Project description:DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes, however, non-CG methylation (mCH) is also detectable in vertebrate tissues, most notably in the nervous system. In mammalian brains, it is well established that: i) mCH is targeted to CAC trinucleotides by DNMT3A, ii) enriched in gene bodies and repetitive elements, and iii) associated with transcriptional repression. However, the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study, we analyse the transcriptomes (RNA-seq) and methylome (RRBS) of developing zebrafish larvae (1-6 weeks) and adult brain (6 month). We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 week old brains
2020-12-18 | E-MTAB-9924 | biostudies-arrayexpress
Project description:We provide raw gene sequences of 174 flowering time regulatory genes and gene othologs across a large barley population (895 barley lines) selected from a collection of landrace, cultivated barley, and research varieties of diverse origin. This set represents the whole variety of cultivated barley lifeforms, namely two- and six-row genotypes with winter, spring, and facultative growth habits. We applied a target capture method based on in-solution hybridization using the myBaits® technology (Arbor Biosciences, Ann Arbour, MI, USA) which is based on in-solution biotinylated RNA probes. Baits were designed for flowering time regulatory genes and gene othologs, and used for production of 80mer capture oligonucleotides for hybridization. Genomic DNA was extracted from leaves of a single two-week old barley plant per variety using the cetyl-trimethyl-ammonium bromide (CTAB) method. Physical shearing of genomic DNA was performed with an average size of 275 bp. Library preparation was conducted with KAPA Hyper Prep Kit (KAPA Biosystems, Wilmington, MA). Hybridization of customised RNA baits with capture pools was performed at 65°C for 24 hours. Each pooled sequence capture library was sequenced on an Illumina HiSeq3000 instrument using three lanes to generate paired-end reads per sample. Genome sequencing was conducted at AgriBio, (Centre for AgriBioscience, Bundoora, VIC, Australia).
2019-02-15 | E-MTAB-7362 | biostudies-arrayexpress
Project description:Alveolar and tissue macrophages were sorted from Schistosoma-exposed and unexposed mice. The mice were C57Bl6/J background. Schistosoma mansoni exposure was intraperitoneal sensitization and intravenous challenge with purified eggs (see Kumar et al. Am J Respir Crit Care Med. 2015;192(8):998-1008. doi: 10.1164/rccm.201410-1820OC. PMID: 26192556). Samples were pooled from N=5 animals per group. Cell sorting was performed on day 3 after IV challenge. Alveolar macrophages were identified as CD45+F4/80+CD11c+SiglecF+. Tissue macrophages were identified as CD45+F4/80+CD11b+SSClow. The RNA library was prepared using a Kappa Stranded mRNA-Seq kit. RNA sequencing was performed on an Ion Proton platform. Expression analysis was performed using Tophat-Bowtie-Cufflinks with Galaxy online.
2016-07-21 | E-GEOD-84651 | biostudies-arrayexpress
Project description:Primary monocyte to macrophage differentiation involves significant changes in chromosome conformation different from cultured THP-1 cells
| PRJEB34065 | ENA
Project description:Primary monocyte to macrophage differentiation involves significant changes in chromosome conformation different from cultured THP-1 cells
| PRJEB34069 | ENA
Project description:Transcriptome exploration of Human Dermal Lymphatic Endothelial Cells
2024-04-01 | E-MTAB-13907 | biostudies-arrayexpress
Project description:During development histone modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origins of the epigenome during embryonic development. Here we generate a comprehensive set of embryonic epigenome reference maps, which we use to determine the extent to which maternal factors shape chromatin state in Xenopus embryos. Using α-amanitin to inhibit zygotic transcription, we find that the majority of H3K4me3 and H3K27me3-enriched regions form a maternally defined epigenetic regulatory space with an underlying logic of hypomethylated islands. This maternal regulatory space extends to a substantial proportion of neurula stage-activated promoters. In contrast, p300-recruitment to distal regulatory regions requires embryonic transcription at most loci. The results show that H3K4me3 and H3K27me3 are part of a regulatory space that exerts an extended maternal control well into post-gastrulation development, and highlight the combinatorial action of maternal and zygotic factors through proximal and distal regulatory sequences. We have performed ChIP-sequencing of eight histone modifications, RNA polymerase II (RNAPII) and the enhancer protein p300 at five stages of development: blastula (st. 9), gastrula (st. 10.5, 12.5), neurula (st. 16) and tailbud (st. 30). These experiments allow identification of enhancers (H3K4me1, p300), promoters (H3K4me3, H3K9ac), transcribed regions (H3K36me3, RNAPII) and repressed and heterochromatic domains (H3K27me3, H3K9me2, H3K9me3, H4K20me3). In addition we generated pre-MBT (st. 8) maps for three histone modifications (H3K4me3, H3K9ac, H3K27me3) and single-base resolution DNA methylome maps using whole genome bisulfite sequencing of blastula and gastrula (st. 9 and 10.5) embryos. To determine the maternal and zygotic contributions to chromatin state, we used alpha-amanitin to block embryonic transcription. Fertilised eggs were injected with 2.3 nl of 2.67 ng/ul alpha-amanitin and developed until the control embryos reached mid-gastrulation. Alpha-amanitin and control embryos were used for RNA-seq and ChIP-seq of RNAPII, H3K4me3, H3K27me3 and p300. For all ChIP-seq samples of the epigenome reference maps and RNAPII ChIP-seq samples of the α-amanitin experiments three biological replicates of different chromatin isolations of 45 embryos were pooled. Two biological replicates for H3K4me3 (α-amanitin injected: resp. 90 and 56 embryo equivalents (eeq); control: resp. 45 and 67 eeq), H3K27me3 (α-amanitin injected: resp. 90 and 180 eeq; control: resp. 45 and 202 eeq) and p300 (α-amanitin injected: resp. 112 and 56 eeq; control: resp. 112 and 67 eeq) ChIP-seq samples of the α-amanitin experiments were generated. For RNA-seq samples of the α-amanitin experiments RNA from 5 embryos from one biological replicate was isolated and depleted of ribosomal RNA
2015-12-15 | E-GEOD-67974 | biostudies-arrayexpress
Project description:Although technological advances now allow increased tumor profiling, a detailed understanding of the mechanisms leading to the development of different cancers remains elusive. Our approach towards understanding the molecular events that lead to cancer is to characterize changes in transcriptional regulatory networks between normal and tumor tissue. Because enhancer activity is thought to be critical in regulating cell fate decisions, we have focused our studies on distal regulatory elements and transcription factors that bind to these elements. Using DNA methylation data, we identified more than 25,000 enhancers that are differentially activated in breast, prostate, and kidney tumor tissues, as compared to normal tissues. We then developed an analytical approach called TENET (Tracing Enhancer Networks using Epigenetic Traits) that correlates DNA methylation levels at enhancers with gene expression to identify more than 800,000 genome-wide links from enhancers to genes and from genes to enhancers. We found more than 1,200 transcription factors to be involved in these tumor-specific enhancer networks. We further characterized several transcription factors linked to a large number of enhancers in each tumor type, including GATA3 in non-basal breast tumors, HOXC6 and DLX1 in prostate tumors, and ZNF395 in kidney tumors. We showed that HOXC6 and DLX1 are associated with different clusters of prostate tumor-specific enhancers and confer distinct transcriptomic changes upon knockdown in C42B prostate cancer cells. We also discovered de novo motifs enriched in enhancers linked to ZNF395 in kidney tumors. Our studies characterized tumor-specific enhancers and revealed key transcription factors involved in enhancer networks for specific tumor types and subgroups. Our findings, which include a large set of identified enhancers and transcription factors linked to those enhancers in breast, prostate, and kidney cancers, will facilitate understanding of enhancer networks and mechanisms leading to the development of these cancers. Examination of FAIRE and ChIP assays in prostate and breast epithelial cells. RNA-seq assays in C42B, prostate cancer cell line after knocking down of TFs (HOXC6, DLX1).
2016-10-26 | E-GEOD-78913 | biostudies-arrayexpress