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New vaccine design approaches would be greatly facilitated by a better understanding of the early systemic changes, and those that occur at the site of injection, responsible for the installation of a durable and oriented protective response. We performed a detailed characterization of very early infection and host response events following the intradermal administration of the modified vaccinia virus Ankara attenuated vaccine in non-human primates. Integrated analysis of the data obtained from in vivo imaging, histology, flow cytometry, multiplex cytokine, and transcriptomic analysis using tools derived from systems biology, such as correlation networks, showed a strong early local and systemic inflammatory response that peaked at 24 h, which was then progressively replaced by an adaptive response during the installation of the host response to the vaccine. Such comprehensive approaches should improve our understanding of how to effectively orientate the immune response, and could contribute to rational vaccine development.
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Cotyledons and leaf transcriptomes of species of Salsoleae with different photosynthetic types were de novo assembled and analyzed to provide a better understanding of differential gene expression between C3, C2 and C4 species. Total RNA of cotyledons and leaves of different species of Salsoleae with different photosynthetic types (C3 Salsola webbii, C2 Salsola divaricata, C4 Salsola oppositifolia, C4 Hammada scoparia) were isolated with RNeasy Plant Mini Kit (Qiagen) following Standard protocol (January 2011) and including DNase Digestion with RNase-Free DNase Set (Qiagen). 500 ng were used for cDNA library generation conducted with TruSeq RNA Sample Preperation Kit (Illumina Inc.) following Low Sample Protocol (TruSeq RNA Sample Preparation v2 Guide, Illumina Proprietary, Part # 15026495 Rev. C, May 2012). Sequencing of single reads was performed on an Illumina HiSeq2000 platform.
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We observed that silencing DLC1 in HUVEC made them more resilient to certain types of cell death. We wondered what type of mechanism is protecting the cells from death induced after long term confluence culture. HUVEC were transduced with the control (pLKO) or silencing vectors shDLC1#3 or #7 (TRCN0000047823, TRCN0000047827; all from Sigma). The cells were grown for different times in optimal culture conditions, and then were grown to full confluence (to a time where cell death was not immediately apparent) and RNA was extracted and studied by microarray
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This experiment was designed to probe the function of Activin/Nodal signalling in the deposition of m6A in human pluripotent stem cells (hPSCs). hPSCs were cultured in presence of Activin or subjected to short-term inhibition of Activin/Nodal signalling for 2h using the receptor antagonist SB-431542 (IP). The global abundance of m6A was then measured by nuclear-enriched methylated RNA immunoprecipitation followed by deep sequencing (NeMeRIP-seq). Pre-NeMeRIP input RNA was used as control to normalise for the changes in gene expression in the two conditions.
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Analysis of Cas9/sgRNA mutagenic activity at a variety of loci in zebrafish. Each loci has a control, where no Cas9/sgRNA were injected. This is amplicon sequencing with Illumina, after PCR amplification. Data was processed with ampliCan R package version 1.1.1.
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In the current study we did microarray of upland rice cultivar Nagina22 for drought stress at reproductive stage (panicle initiation) and analyzed drought stress responsive genes. We have taken flag leaf for our study as it is most essential organ for photosynthesis in rice. Normal watering Vs Drought Stress Flag leaf of Control (Three biological replicates) plant of Nagina22: C1, C2, C3 Flag leaf of drought stressed (Three biological replicates) plant of Nagina 22: S1, S2, S3
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Transcriptional profiles were compared between wild type and the srk2abgh mutant under a dehydration stress condition.
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RNAseq from Illumina MiSeq 75bp paired end for transcriptome assembly. The following tissue samples were pooled: skeletal muscle; kidney; spleen; ovaries; placenta; castor gland; tail; toe webbing; whole blood; brain; lung; liver; heart; stomach; tongue; intestine
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DNA microarray analysis was performed on RNA from a strain of Mycobacterium tuberculosis H37Rv in which the essential whiB1 gene was deleted from the chromosome but partially complemented by a wild type allele on a plasmid, compared to RNA from H37Rv wild type containing the same plasmid.
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To unravel the fine architecture of neocentromeres found in three well-differentiated liposarcoma (WDLPS) cell lines as patchworks of multiple short amplified sequences, disclosing a much more higher complexity than previously reported. Next generation sequencing data (WGS, RNA-seq, CENP-A/ChIP-seq) are available at the Sequence Read Archive (BioProject ID: PRJNA378952).
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