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71 results for “Nuclear speckles”
Deconvolved STED nanoscopy images of the nuclear phosphatidylinositol 4,5-bisphosphate and nuclear speckle marker SON together with deconvolved confocal images of DAPI stained nuclei in human formalin-fixed paraffin-embedded skin warts sections
<p>The collection and analysis of formalin-fixed paraffin-embedded (FFPE) human skin sections was approved by the local ethics-committee at the Department of Pathology, University of Cologne, Germany. Written informed consentwas obtained from all patients in accordance with the Declaration of Helsinki. For biopsy materials from archival paraffin blocks of human skin, an informed consent was obtained from all the subjects and ethical approval obtained from the Ethics Committee at the University of Cologne. Surgically removed human FFPE skin biopsies were sectioned into 4 µm sections. Sections were dewaxed, and indirectly immunofluorescently labeled against nuclear phosphatidylinositol 4,5-bisphosphate (nPI(4,5)P2) using 5 µg/mL rabbit primary polyclonal antibody (Echelon Biosciences Inc. Z-A045, clone 2C11). The primary antibody against nPI(4,5)P2 was recognized by the goat secondary antibody conjugated with Abberrior Star 635P (Abberior 2-0002-007-5). Sections were indirectly immunofluorescently labeled against nuclear speckle marker SON using 1 µg/mL rabbit primary polyclonal antibody (Abcam ab121759). The primary antibody against SON was recognized by the goat secondary antibody conjugated with Abberrior Star 580 (Abberrior ST580-1002). Sections were co-stained by DAPI 1:1000 in PBS for 5 min.</p> <p>Imaging of nPI(4,5)P2-635P channel was performed on Leica TCS SP8 STED 3x inverted DMi8 microscope with pulsed white light laser 470-640 nm 1.5 mW and 775 nm pulse STED laser >1.5 W controlled by Leica Application Suite X software and equipped with HC PL APO CS2 100x/1.40 OIL objective used with Leica Type F immersion oil n=1.518. Unidirectional xyz scanning speed was 400 Hz, line accumulation 8. Pixel size was 20 nm in X and Y. Channel settings: 7% 633 nm laser; 775 Notch filter; 50% 775 nm STED laser; 30% 3D STED; HyD 639-698 nm, photon-counting mode, gain 100, gating 0.3-10 ns. Imaging of SON-580 channel was performed on Leica TCS SP8 STED 3x inverted DMi8 microscope with pulsed white light laser 470-640 nm 1.5 mW and 775 nm pulse STED laser >1.5 W controlled by Leica Application Suite X software and equipped with HC PL APO CS2 100x/1.40 OIL objective used with Leica Type F immersion oil n=1.518. Unidirectional xyz scanning speed was 400 Hz, line accumulation 8. Pixel size was 20 nm in X and Y. Channel settings: 10% 585 nm laser; 775 Notch filter; 80% 775 nm STED laser, 30% 3D STED; Hybrid detector (HyD) 589-616 nm, photon-counting mode, gain 100, gating 0.4-10 ns.</p> <p>Z-stacks of STED images were deconvolved using Huygens Professional 22.10 software (Scientific Imaging B.V.). Data sets were processed using Workflow Processor. The workflow consisted of selecting images, setting up the microscopy and deconvolution parameters and saving deconvolved images as 8-bit TIFF single files for individual channels (which were later used for the quantitative analyses; see below). Microscopy parameters were optimized and set as follows. Sampling intervals were ≤20 nm in X and Y and ≤20 nm in Z. Numerical aperture was 1.4; refractive indexes of the lens immersion oil was 1.518 and of the embedding media 1.458; objective quality was good, coverslip position was 0 µm and imaging direction was downward. For nPI(4,5)P2-635P STED channel the backprojected pinhole was 216 nm; excitation (ex.) and emission (em.) wavelengths (λ) were 633 and 651 nm, resp., ex. fill factor 2. STED depletion mode was pulsed, saturation factor 25, STED λ = 775, STED immunity factor 10 and STED 3X was 30%. Classic MLE algorithm with stabilization of Z-slices was used and signal-to-noise ratio was 5.1. For SON-580 STED channel the backprojected pinhole was 195 nm; excitation (ex.) and emission (em.) wavelengths (λ) were 585 and 602 nm, resp., ex. fill factor 2. STED depletion mode was pulsed, saturation factor 20, STED λ = 775, STED immunity factor 10 and STED 3X was 30%. Classic MLE algorithm with stabilization of Z-slices was used and signal-to-noise ratio was 4.</p>
Deconvolved STED nanoscopy images of the nuclear phosphatidylinositol 4,5-bisphosphate and nuclear speckle marker SON together with deconvolved confocal images of DAPI stained nuclei in human formalin-fixed paraffin-embedded skin sections
<p>The collection and analysis of formalin-fixed paraffin-embedded (FFPE) human skin sections was approved by the local ethics-committee at the Department of Pathology, University of Cologne, Germany. Written informed consentwas obtained from all patients in accordance with the Declaration of Helsinki. For biopsy materials from archival paraffin blocks of human skin, an informed consent was obtained from all the subjects and ethical approval obtained from the Ethics Committee at the University of Cologne. Surgically removed human FFPE skin biopsies were sectioned into 4 µm sections. Sections were dewaxed, and indirectly immunofluorescently labeled against nuclear phosphatidylinositol 4,5-bisphosphate (nPI(4,5)P2) using 5 µg/mL rabbit primary polyclonal antibody (Echelon Biosciences Inc. Z-A045, clone 2C11). The primary antibody against nPI(4,5)P2 was recognized by the goat secondary antibody conjugated with Abberrior Star 635P (Abberior 2-0002-007-5). Sections were indirectly immunofluorescently labeled against nuclear speckle marker SON using 1 µg/mL rabbit primary polyclonal antibody (Abcam ab121759). The primary antibody against SON was recognized by the goat secondary antibody conjugated with Abberrior Star 580 (Abberrior ST580-1002). Sections were co-stained by DAPI 1:1000 in PBS for 5 min.</p> <p>Imaging of nPI(4,5)P2-635P channel was performed on Leica TCS SP8 STED 3x inverted DMi8 microscope with pulsed white light laser 470-640 nm 1.5 mW and 775 nm pulse STED laser >1.5 W controlled by Leica Application Suite X software and equipped with HC PL APO CS2 100x/1.40 OIL objective used with Leica Type F immersion oil n=1.518. Unidirectional xyz scanning speed was 400 Hz, line accumulation 8. Pixel size was 20 nm in X and Y. Channel settings: 7% 633 nm laser; 775 Notch filter; 50% 775 nm STED laser; 30% 3D STED; HyD 639-698 nm, photon-counting mode, gain 100, gating 0.3-10 ns. Imaging of SON-580 channel was performed on Leica TCS SP8 STED 3x inverted DMi8 microscope with pulsed white light laser 470-640 nm 1.5 mW and 775 nm pulse STED laser >1.5 W controlled by Leica Application Suite X software and equipped with HC PL APO CS2 100x/1.40 OIL objective used with Leica Type F immersion oil n=1.518. Unidirectional xyz scanning speed was 400 Hz, line accumulation 8. Pixel size was 20 nm in X and Y. Channel settings: 10% 585 nm laser; 775 Notch filter; 80% 775 nm STED laser, 30% 3D STED; Hybrid detector (HyD) 589-616 nm, photon-counting mode, gain 100, gating 0.4-10 ns.</p> <p>Z-stacks of STED images were deconvolved using Huygens Professional 22.10 software (Scientific Imaging B.V.). Data sets were processed using Workflow Processor. The workflow consisted of selecting images, setting up the microscopy and deconvolution parameters and saving deconvolved images as 8-bit TIFF single files for individual channels (which were later used for the quantitative analyses; see below). Microscopy parameters were optimized and set as follows. Sampling intervals were ≤20 nm in X and Y and ≤20 nm in Z. Numerical aperture was 1.4; refractive indexes of the lens immersion oil was 1.518 and of the embedding media 1.458; objective quality was good, coverslip position was 0 µm and imaging direction was downward. For nPI(4,5)P2-635P STED channel the backprojected pinhole was 216 nm; excitation (ex.) and emission (em.) wavelengths (λ) were 633 and 651 nm, resp., ex. fill factor 2. STED depletion mode was pulsed, saturation factor 25, STED λ = 775, STED immunity factor 10 and STED 3X was 30%. Classic MLE algorithm with stabilization of Z-slices was used and signal-to-noise ratio was 5.1. For SON-580 STED channel the backprojected pinhole was 195 nm; excitation (ex.) and emission (em.) wavelengths (λ) were 585 and 602 nm, resp., ex. fill factor 2. STED depletion mode was pulsed, saturation factor 20, STED λ = 775, STED immunity factor 10 and STED 3X was 30%. Classic MLE algorithm with stabilization of Z-slices was used and signal-to-noise ratio was 4.</p>
Disruption of nuclear speckle integrity dysregulates RNA splicing in C9ORF72-FTD/ALS
GEO Series GSE248404. Homo sapiens. 15 samples. Type: Expression profiling by high throughput sequencing.
Nuclear speckles regulate functional programs in cancer (RNA SART1, DDX39A, SARNP, FIBP, TMEM259 kd)
GEO Series GSE269570. Homo sapiens. 26 samples. Type: Expression profiling by high throughput sequencing.
mRNA export factors store nascent transcripts within nuclear speckles as an adaptive response to transient global inhibition of transcription.
GEO Series GSE183571. Homo sapiens. 50 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
mRNA export factors store nascent transcripts within nuclear speckles as an adaptive response to transient global inhibition of transcription.
GEO Series GSE183569. Homo sapiens. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Nuclear speckles regulate functional programs in cancer (CnR)
GEO Series GSE248706. Homo sapiens. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Phosphorylation controls mRNA retention via nuclear speckle cohesion - APEX2-seq
GEO Series GSE240891. Homo sapiens. 64 samples. Type: Expression profiling by high throughput sequencing.
DNA methylation insulates exons from CTCF loops with nuclear speckles (ChiP-Seq)
GEO Series GSE217752. Homo sapiens. 39 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
TAF2 condensation in nuclear speckles links basal transcription factor TFIID to RNA splicing factors
GEO Series GSE254081. Homo sapiens. 39 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
TAF2 condensation in nuclear speckles links basal transcription factor TFIID to RNA splicing factors [CUT&RUN]
GEO Series GSE254080. Homo sapiens. 30 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Nuclear speckles regulate functional programs in cancer (RNA PT2399)
GEO Series GSE248709. Homo sapiens. 10 samples. Type: Expression profiling by high throughput sequencing.
mRNA export factors store nascent transcripts within nuclear speckles as an adaptive response to transient global inhibition of transcription.
GEO Series GSE183570. Homo sapiens. 28 samples. Type: Expression profiling by high throughput sequencing.
CTCF/cohesin organize the ground state of chromatin-nuclear speckle association [RNA-Seq]
GEO Series GSE248102. Homo sapiens. 59 samples. Type: Expression profiling by high throughput sequencing.
CTCF/cohesin organize the ground state of chromatin-nuclear speckle association [hela rad21-aid RNA-seq]
GEO Series GSE273618. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
CTCF/RAD21 organize the ground state of chromatin-nuclear speckle association
GEO Series GSE248103. Homo sapiens. 135 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
DNA methylation insulates exons from CTCF loops with nuclear speckles
GEO Series GSE217760. Homo sapiens. 99 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other.
Stress-induced splicing activation of immediate early genes by nuclear speckle reorganization
GEO Series GSE231521. Homo sapiens. 36 samples. Type: Expression profiling by high throughput sequencing.
Stress-induced splicing activation of immediate early genes by nuclear speckle reorganization [ThioU]
GEO Series GSE231520. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
Dynamics of RNA localization to nuclear speckles are connected to splicing efficiency
GEO Series GSE255208. Homo sapiens. 40 samples. Type: Expression profiling by high throughput sequencing; Other.
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