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1,418 results for “mutant expressivity”
Transcriptome analysis of the effect of over-expressing H2A.J mutants in proliferating WI38 fibroblasts for the paper entitled: The H2A.J histone variant contributes to Interferon-Stimulated Gene expression in senescence by its weak interaction with H1 and the derepression of repeated DNA sequences
<p>Abstract for overall study:</p> <p>The histone variant H2A.J was previously shown to accumulate in senescent human fibroblasts with persistent DNA damage to promote inflammatory gene expression, but its mechanism of action was unknown. We show that H2A.J accumulation contributes to weakening the association of histone H1 to chromatin and increasing its turnover. Decreased H1 in senescence is correlated with increased expression of some repeated DNA sequences, increased expression of STAT/IRF transcription factors, and transcriptional activation of Interferon-Stimulated Genes (ISGs). The H2A.J-specific Val-11 moderates the transcriptional activity of H2A.J, and H2A.J-specific Ser-123 can be phosphorylated in response to DNA damage with potentiation of its transcriptional activity by the phospho-mimetic S123E mutation. Our work demonstrates the functional importance of H2A.J-specific residues and potential mechanisms for its function in promoting inflammatory gene expression in senescence.</p> <p>Specific description for this dataset:</p> <p>H2A.J differs from canonical H2A only by a valine at position 11 instead of alanine, and the 7 C-terminal amino acids containing a potential minimal phosphorylation site SQ for DNA-damage response kinases. To test the functional importance of these H2A.J-specific sequences, we mutated Val-11 to Ala as is found in all canonical H2A sequences, and we mutated Ser-123 to either Glu to mimic a phospho-serine residue or to Ala to prevent phosphorylation. We also substituted the C-terminus of H2A.J with the C-terminus of H2A. These mutants, WT-H2A.J and canonical H2A-type1 were ectopically expressed in proliferating fibroblasts, and their microarray transcriptomes were compared to that of proliferating and senescent fibroblasts without ectopic histone expression. Genome-wide transcriptome analysis indicated that senescent fibroblasts clustered distinctly from proliferating fibroblasts, and proliferating fibroblasts expressing the H2A.J-V11A and H2A.J-S123E mutants clustered distinctly from fibroblasts expressing the other H2A.J mutants, WT-H2A.J, and H2A. Hallmark gene set enrichment analysis of the transcriptomes of fibroblasts expressing H2A.J-V11A or H2A.J-S123E versus control proliferating fibroblasts indicated that they showed the same highly significant enrichment for the Epithelial-Mesenchyme Transition, TNF-Alpha Signaling Via NF-kB, and Inflammatory Response gene sets. Notable inflammatory genes including IL1A, IL1B, IL6, CXCL8, and CCL2 are contained in these gene sets and are often induced in senescence as part of the senescence-associated secretory phenotype. Heat maps showed that the H2A.J-V11A and H2A.J-S123E mutants were particularly apt at activating the expression of these inflammatory genes in proliferating fibroblasts</p>
Effect of shade and nitrogen content on Arabidopsis Col-0 and cytokinin mutants abcg14 and cypDM mRNA-seq gene expression processed tables.
<p>This dataset is an add-on for Gautrat et al., containing processed files for the mRNAseq data in tab delimited txt format.</p> <p>Here, you can obtain the raw counts file, the normalized CPM values, and the normalized logCPM values</p> <p>The RNA-seq raw data supporting the conclusions of this article have been deposited in ArrayExpress (Kolesnikov et al., 2015) at EMBL-EBI (www.ebi.ac.uk/arrayexpress), under accession numbers E-MTAB-13638.</p> <p>All relevant custom r scripts are available at https://github.com/aromanowski/shade_N_ck</p>
LC-MS/MS data for WT human PANX1 with or without co-expressing Src-Y529F mutant
<p>Protein phosphorylation is one of the major molecular mechanisms regulating protein activity and function throughout the cell. Pannexin 1 (PANX1) is a large-pore channel permeable to ATP and other cellular metabolites. Its tyrosine phosphorylation and subsequent activation have been found to play critical roles in diverse cellular conditions, including neuronal cell death, acute inflammation, and smooth muscle contraction. Specifically, the non-receptor kinase Src has been reported to phosphorylate Tyr198 and Tyr308 of mouse PANX1 (equivalent to Tyr199 and Tyr309 of human PANX1), resulting in channel opening and ATP release. Although the Src-dependent PANX1 activation mechanism has been widely discussed in the literature, independent validation of the tyrosine phosphorylation of PANX1 has been lacking. Here, we show that commercially available antibodies against the two phosphorylation sites mentioned above—which were used to identify endogenous PANX1 phosphorylation at these two sites—are nonspecific and should not be used to interpret results related to PANX1 phosphorylation. We further provide evidence that neither tyrosine residue is a major phosphorylation site for Src kinase in heterologous expression systems. We call on the field to re-examine the existing paradigm of tyrosine phosphorylation-dependent activation of the PANX1 channel.</p>
Gene expression for suboptimal mycorrhizal colonization in wild-type and jasmonic acid deficient spr2 tomato mutants
<pre>Data were obtained from mycorrhizhal colonized roots of wild-type and and spr2 mutants tomato plants, at 32 and 45 days after mycorrhizhal inoculation. Amplifications were performed using SYBR Green detection chemistry and run in triplicate in 96-well reaction plates with the CFX96 Touch Real-Time PCR Detection System (Bio-Rad, Hercules, CA, USA). The data was analyzed by the delta delta ct method. </pre>
LC-MS/MS data for WT human PANX1 with or without co-expressing Src-Y529F mutant
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RNA-Seq data of Raji cells transduced with retrovirus expressing WT or mutant IRF4
<p>Total RNA was extracted using RNAiso Plus (TaKaRa) from Raji cells transduced with retrovirus expressing WT or mutant IRF4. RNA-seq was performed by BGI (Beijing Genomic Institute, ShenZhen, China) using the BGISEQ-500 platform, pair end 100 bases read lengths. The sequencing data were filtered with SOAPnuke (v1.5.2). The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). After that, Ericscript (v0.5.5) and rMATS (V3.2.5) were used to identify genes and differentially spliced genes (DSGs), respectively. Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database for this organism built by BGI with known and novel coding transcripts included, then the expression level of gene was calculated by RSEM (v1.2.12).</p>
Data from: No evidence for induction or selection of mutant sodium channel expression in the copepod Acartia husdsonica challenged with the toxic dinoflagellate Alexandrium fundyense
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Expression Data human IDH1 mutant and wild-type high grade gliomas
GEO Series GSE104722. Homo sapiens. 20 samples. Type: Expression profiling by array.
Gene expression signature of WT siblings and hif1α mutants in normoxia and after hypoxia chamber incubation
GEO Series GSE89117. Danio rerio. 4 samples. Type: Expression profiling by array.
Next-generation sequencing analyses of the differently expressed genes of wild type and atcep1 mutant Arabidopsis thaliana
GEO Series GSE50956. Arabidopsis thaliana. 6 samples. Type: Expression profiling by high throughput sequencing.
Expression data in an Arabidopsis cytokinin (CK)-signaling mutant, ahp2,3,5 and its wild type plant (Col-0) under drought and well-water (control) conditions.
GEO Series GSE42290. Arabidopsis thaliana. 12 samples. Type: Expression profiling by array.
Bulk gene expression profiles of adult antennae in wild-type and orco mutant Harpegnathos saltator
GEO Series GSE236790. Harpegnathos saltator. 12 samples. Type: Expression profiling by high throughput sequencing.
Identification of differentially expressed genes in the mutant tail regression failed (trf) in Ciona intestinalis.
GEO Series GSE124672. Ciona intestinalis. 8 samples. Type: Expression profiling by array.
RNA sequencing of exogenous RNAi mutants under CPL-1* expression
GEO Series GSE202291. Caenorhabditis elegans. 12 samples. Type: Expression profiling by high throughput sequencing.
Differential gene expression in the grf10Δ mutant of Candida albicans in high copper containing growth medium
GEO Series GSE223217. Candida albicans. 12 samples. Type: Expression profiling by high throughput sequencing.
Genome-wide occupancy of Tcf7l2/Tcf4 in rat and expression profiling of Tcf7l2 mutant and control mice
GEO Series GSE65120. Rattus norvegicus; Mus musculus. 5 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Comparison of the expression profiles of the 630E strain and a sigF mutant after 14h of growth
GEO Series GSE43199. Clostridioides difficile. 4 samples. Type: Expression profiling by array.
Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [bulkRNA-seq]
GEO Series GSE275536. Danio rerio. 6 samples. Type: Expression profiling by high throughput sequencing.
Genome wide analysis of transcriptome modification after re-expression of PBRM1 WT and its BAH domain mutant in PBRM1 CRISPR-KO HEK293T cells.
GEO Series GSE149874. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
Detection of mutant NPM1 mRNA in acute myeloid leukemia (AML) using custom gene expression arrays [Training cohort]
GEO Series GSE42194. Homo sapiens. 505 samples. Type: Other.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.