Oncomelania hupensis hupensis isolate:GD
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ABSTRACT:
PROVIDER: PRJNA552664 | ENA |
REPOSITORIES: ENA
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Project description:Oncomelania hupensis hupensis Raw sequence reads
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Project description:Innate-like gd T effector subsets are exported from the thymus as “memory-like” cells prewired for rapid, specialized function. Previously, we showed that emergent gd subsets distinguished by TCRg and TCRd usage in the fetal and adult thymus possess distinct global transcriptomes and the subset-specific combinatorial expression of High Mobility Group box transcription factors (HMG TFs) shown as a primary determinant of gd effector differentiation. While the detailed mechanism of HMG TFs cooperativity and counter-regulations are not fully understood, a key feature for IL-17 producing gd T effectors (Tgd 17) is predicted to be context-dependent interactions between SOX13 and TCF1 that result in diversified target gene regulation. Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATACseq) will map chromatin accessibility genome wide. Each read will provide information about the positions of nucleosomes and nucleosome-free regions.
2018-11-01 | GSE74637 | GEO
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Project description:We performed chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-seq) for ICN1 in thymic gd T cells from neonates of C57BL/6 mice. Sequence reads for ICN1 and Input were aligned with the mouse reference genome (mm10) by bowtie program (v1.0.0), and peak detection and identification of ICN1 binding sites were obtained with MACS program (v1.4.2). ChIP-seq data revealed that 12%, 6% and 47% of ICN1 binding sites were within -10kb upstream of transcription start site, +10kb downstream of 3'end and the bodies of genes, respectively. The other of ICN1 binding sites was intergenic. We also found that ICN1 directly bound -5.4kb upstream of transcript start site of IL-7 receptor alpha (IL-7Ra) locus, which were estimated as a new promoter region of IL-7Ra. Some of ICN1 binding sites (e.g. TCF1 promoter) were consistent with previous reports, but others (e.g. Nr4a1 promoter) were novel. These suggests that ICN1 was associated with a lot of transcriptional regulation in gd T cells. Examination of ICN1 binding sites in gd T cells
2014-11-14 | E-GEOD-56756 | biostudies-arrayexpress
Project description:gd T cells are major innate sources of interleukin-17 (IL-17) and interferon-g (IFN-g), which are differentially produced by two thymically-derived subsets segregated on CD27 expression. However, the molecular mechanisms that program the functional differentiation of gd cells remain incompletely understood. Here we show that CD27+ gd cells are epigenetically committed to express Ifng but not Il17, whereas CD27- gd cells spontaneously make IL-17 but can be induced to produce IFN-g under specific inflammatory conditions. This M-bM-^@M-^\plasticM-bM-^@M-^] behavior of CD27- gd cells associates with permissive histone H3 marks at loci encoding Ifng and upstream M-bM-^@M-^\type 1M-bM-^@M-^] transcription factors. By contrast, Il17 and related M-bM-^@M-^\type 17M-bM-^@M-^] factors are epigenetically and transcriptionally active in CD27- but silenced in CD27+ gd cells. Hence, stable versus plastic behaviors of gd cell subsets are controlled by integrated epigenetic and transcriptional mechanisms that regulate the expression of M-bM-^@M-^\masterM-bM-^@M-^] transcription factors and effector cytokine genes. ChIP was carried out on FACS-sorted cells from pooled spleen/ lymph nodes. The following antibodies were used: anti-histone H3K4me2 (07-030, Millipore) and anti-histone H3k27me3 (07-449, Millipore). Between 105 - 106 cells were crosslinked with formaldehyde and nuclei were isolated and sonicated with a Sanyo Soniprep 150 at an amplitude of 10 microns with 17 times 10s bursts, resulting in 200M-bM-^@M-^S400bp chromatin fragments. IP was carried out as previously described 49. The Immunoprecipitated DNA released from crosslinked proteins was extracted with the QiaQuick kit (Qiagen) in accordance with the manufacturerM-BM-4s instructions. Deep sequencing was performed at the GeneCore facility of EMBL (http://www.genecore.embl.de/). At least 1 ng of immunoprecipitated DNA was used for library preparation according to the Illumina protocol.
2013-09-01 | E-GEOD-42098 | biostudies-arrayexpress