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434 results for “Histone Acetylation”
X-ray diffraction images for DPF3 tandem PHD fingers co-crystallized with an acetylated histone-derived peptide
<p>This submission includes a tar archive of bzipped diffraction images recorded with the ADSC Q315r detector at the Advanced Photon Source of Argonne National Laboratory, Structural Biology Center beam line 19-ID. Relevant meta data can be found in the headers of those diffraction images.</p> <p>Please find below the content of an input file XDS.INP for the program XDS (Kabsch, 2010), which may be used for data reduction. The "NAME_TEMPLATE_OF_DATA_FRAMES=" item inside XDS.INP may need to be edited to point to the location of the downloaded and untarred images.</p> <p>!!! Paste lines below in to a file named XDS.INP</p> <p>DETECTOR=ADSC MINIMUM_VALID_PIXEL_VALUE=1 OVERLOAD= 65000<br /> DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0<br /> DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0<br /> TRUSTED_REGION=0.0 1.05<br /> MAXIMUM_NUMBER_OF_JOBS=10<br /> ORGX= 1582.82 ORGY= 1485.54<br /> DETECTOR_DISTANCE= 150<br /> ROTATION_AXIS= -1.0 0.0 0.0<br /> OSCILLATION_RANGE=1<br /> X-RAY_WAVELENGTH= 1.2821511<br /> INCIDENT_BEAM_DIRECTION=0.0 0.0 1.0<br /> FRACTION_OF_POLARIZATION=0.90<br /> POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0<br /> SPACE_GROUP_NUMBER=20<br /> UNIT_CELL_CONSTANTS= 100.030 121.697 56.554 90.000 90.000 90.000<br /> DATA_RANGE=1 180<br /> BACKGROUND_RANGE=1 6<br /> SPOT_RANGE=1 3<br /> SPOT_RANGE=31 33<br /> MAX_CELL_AXIS_ERROR=0.03<br /> MAX_CELL_ANGLE_ERROR=2.0<br /> TEST_RESOLUTION_RANGE=8.0 3.8<br /> MIN_RFL_Rmeas= 50<br /> MAX_FAC_Rmeas=2.0<br /> VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= 6000 30000<br /> INCLUDE_RESOLUTION_RANGE=50.0 1.7<br /> FRIEDEL'S_LAW= FALSE<br /> STARTING_ANGLE= -100 STARTING_FRAME=1<br /> NAME_TEMPLATE_OF_DATA_FRAMES= ../x247398/t1.0???.img</p> <p>!!! End of XDS.INP</p> <p> </p> <p> </p>
Chemical perturbations impacting histone acetylation regulate colorectal cancer differentiation
<p>M60.count.Rdata: Rdata that includes the raw count, scaled CPM value and meta data of each sample. (Fig. 1 & 4)</p> <p>DAP.merged.Log2FC.csv: integrated DiffBind results that shows the log2FC and P-value/FDR of peaks. (Fig. 1 & 4)</p> <p>rawdata_scRNA-seq.zip: raw count data of scRNA-seq data from cellranger (labels: A: DMSO, B: MRK60, D: MRK60 + JQAD1). (Fig. 5)</p>
Chromatin regulation by Histone H4 acetylation at Lysine 16 during cell death and differentiation in the myeloid compartment
<p>Histone H4 acetylation at Lysine 16 (H4K16ac) is a key epigenetic mark involved in gene regulation, DNA repair and chromatin remodeling, and though it is known to be essential for embryonic development, its role during adult life is still poorly understood. Here we show that this lysine is massively hyperacetylated in peripheral neutrophils. Genome-wide mapping of H4K16ac in terminally differentiated blood cells, along with functional experiments, supported a role for this histone post-translational modification in the regulation of cell differentiation and apoptosis in the hematopoietic system. Furthermore, in neutrophils, H4K16ac was enriched at specific DNA repeats. These DNA regions presented an accessible chromatin conformation and were associated with the cleavage sites that generate the 50 kb DNA fragments during the first stages of programmed cell death. Our results thus suggest that H4K16ac plays a dual role in myeloid cells as it not only regulates differentiation and apoptosis, but it also exhibits a non-canonical structural role in poising chromatin for cleavage at an early stage of neutrophil cell death.</p> <p> </p>
Ultra-Accurate Correlation Between Precursor and Fragment Ions in Two-lDimensional Mass Spectrometry: Acetylated vs. Trimethylated Histone Peptides
<p>Two-dimensional mass spectrometry (2D MS) is a method<br> for tandem<br> mass spectrometry in which precursor and fragment ions are correlated<br> by manipulating ion radii rather than by ion isolation. A 2D mass<br> spectrum contains the fragmentation patterns of all analytes in a<br> sample, acquired in parallel. We report ultrahigh-resolution narrowband<br> 2D mass spectra of a mixture of two histone peptides with the same<br> sequence, one of which carries an acetylation and the other a trimethylation<br> (m/z 0.006 difference). We reduced<br> the distance between data points in the precursor ion dimension and<br> compared the accuracy of the precursor-fragment correlation with the<br> resolving power. We manage to perform label-free quantification on<br> the histone peptide mixture and show that precursor and fragment ions<br> can be accurately correlated even though the precursor ions are not<br> resolved. Finally, we show that increasing the resolution of a 2D<br> mass spectrum in the precursor ion dimension too far can lead to a<br> decline in the signal-to-noise ratio.</p>
Histone acetylation readers Bdf1 and Yaf9 direct SWR1 remodeler to +1 nucleosome
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Supplementary tables for: CHAS, a deconvolution tool, infers cell type-specific signatures in bulk brain histone acetylation studies of brain disorders
<p>Supplementary tables for: CHAS, a deconvolution tool, infers cell type-specific signatures in bulk brain histone acetylation studies of brain disorders. </p> <p>Supplementary Table 1: S1_AD_H3K27ac_Marzi2018_CHAS_analysis.xls, includes the sample metadata, differentially acetylated regions when controlling for CHAS scores and CHAS-MF cell type proportions, GO enrichment analysis results using the two sets of differentially acetylated regions. </p> <p>Supplementary Table 2: S2_PD_H3K27ac_Toker2022_CHAS_analysis.xls, includes the sample metadata, differentially acetylated regions when controlling for CHAS scores and CHAS-MF cell type proportions.</p> <p>Supplementary Table 3: S3_ASD_H3K27ac_Sun2016_CHAS_analysis.xls, includes the sample metadata, differentially acetylated regions when controlling for CHAS scores and CHAS-MF cell type proportions for the prefrontal cortex and the cerebellum, GO enrichment analysis results using the two sets of differentially acetylated regions in the prefrontal cortex. </p> <p>Supplementary Table 4: S4_SCZ_BPD_H3K27ac_Girdhar2022_CHAS_analysis.xls, includes the sample metadata, differentially acetylated regions when controlling for CHAS scores and CHAS-MF cell type proportions, GO enrichment analysis results using the two sets of differentially acetylated regions. </p> <p> </p> <p> </p> <p> </p> <p> </p>
Data from: Lysine-14 acetylation of histone H3 in chromatin confers resistance to the deacetylase and demethylase activities of an epigenetic silencing complex
The core CoREST complex (LHC) contains histone deacetylase HDAC1 and histone demethylase LSD1 held together by the scaffold protein CoREST. Here we analyze the purified LHC with modified peptide and reconstituted semisynthetic mononucleosome substrates. LHC demethylase activity toward methyl-Lys4 in histone H3 is strongly inhibited by H3 Lys14 acetylation, and this appears to be an intrinsic property of the LSD1 subunit. Moreover, the deacetylase selectivity of LHC unexpectedly shows a marked preference for H3 acetyl-Lys9 versus acetyl-Lys14 in nucleosome substrates but this selectivity is lost with isolated acetyl-Lys H3 protein. This diminished activity of LHC for Lys14 deacetylation in nucleosomes is not merely due to steric accessibility based on the pattern of sensitivity of the LHC enzymatic complex to hydroxamic acid-mediated inhibition. Overall, these studies have revealed how a single Lys modification can confer a composite of resistance in chromatin to a key epigenetic enzyme complex involved in gene silencing.
Data from: Lysine-14 acetylation of histone H3 in chromatin confers resistance to the deacetylase and demethylase activities of an epigenetic silencing complex
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Histone acetylation in wild-type and SET2 deletion yeast strains
GEO Series GSE28097. Saccharomyces cerevisiae. 24 samples. Type: Genome binding/occupancy profiling by genome tiling array.
Toll-like receptor signaling rewires macrophage metabolism and promotes histone acetylation via ATP-citrate lyase
GEO Series GSE129497. Mus musculus. 9 samples. Type: Expression profiling by high throughput sequencing.
ChIP-Seq analysis of Histone H3 acetylation (K27) changes in response to vasopressin in mouse renal collecting duct mpkCCD cells
GEO Series GSE95007. Mus musculus. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Histone acetylation regulates intracellular pH
GEO Series GSE40114. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
RNA sequencing data of Kat6a (Moz) mutant embryonic mouse hearts (ING4 and ING5 are essential for histone H3 lysine 14 acetylation and epicardial cell lineage development)
GEO Series GSE246402. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
Novel contribution of acetylated histone variant H2A.Z in activation of neo-enhancers in prostate cancer [ChIP-seq]
GEO Series GSE76336. Homo sapiens. 28 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Pathophysiological Significance of Impaired KAT7-Dependent Histone H3K14 Acetylation During Zinc Deficiency [RNA-seq]
GEO Series GSE288563. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Jasmonates and Histone deacetylase 6 activate Arabidopsis genome-wide histone acetylation and methylation during the early acute stress response
GEO Series GSE197733. Arabidopsis thaliana. 23 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Gas41 links histone acetylation to H2A.Z deposition and stem cell identity maintenance
GEO Series GSE100460. Mus musculus. 27 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
Histone 3 K9 and K27 acetylation of enhancers in response to thyroid hormone
GEO Series GSE128535. Mus musculus. 56 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
De novo mutations of MSL3 cause a novel X-linked syndrome due to impaired histone H4 lysine 16 acetylation
GEO Series GSE102250. Homo sapiens. 16 samples. Type: Expression profiling by high throughput sequencing.
Chromatin accessibility, p300 and histone acetylation define PML-RARalpha- and AML1-ETO-binding sites
GEO Series GSE30254. Homo sapiens. 25 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
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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.
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