Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
382
datasets available to search
ShareScore release 0.7.1
Dataset results
382 results for “red cells”
Ditrect STORM imaging and image reconstruction of the transcription initiation marker P-S5 and nuclear PI(4,5)P2 indirectly immunolabeled with AF647 (red) and AF555 (green) in control cells.
<p>U-2 OS cells were grown in DMEM with 10% FBS at 37°C and 5% CO<sub>2</sub>. Cells were plated one day before staining in ~50% confluence on the high-precision 12 mm round coverslips treated with Hellmanex, sonicated, washed, dried and sterilized. Cells were control treated with 1:000 DMSO in the culture media.</p> <p>U2OS cells were washed twice with PBS (pH 7.4) and fixed for 30 min in 2% PFA in PBS, washed 3-times for 5 min with PBS, then permeabilized in 0.1% Triton X-100 in PBS for 20 min, washed 3-times for 5 min by PBS and blocked in filtered 5% BSA in PBS for 30 min. Cells were incubated for 45 min with rabbit polyclonal IgG anti-RNAPII CTD P-S5 (Abcam ab5131) 3 µg/mL and mouse ascites IgM anti-PI(4,5)P2 2C11 (Z-A045; Echelon Biosci. Inc., USA) 5 µg/mL in 5% BSA in PBS, washed 3-times for 5 min in PBS and incubated for 30 min with goat anti-mouse IgM (µ-chain) AF555 (Jackson ImmunoRes. A24126) 10 µg/mL; goat anti-rabbit IgG AF647 (Invitrogen A21245) 10 µg/mL diluted in 5% BSA in PBS. Then the cells were washed 3-times for 5 min in PBS, post-fixed for 15 min in 2% PFA in PBS and washed 3-times for 5 min in PBS. All procedures were performed at RT and the cells were stored in PBS in the fridge overnight prior imaging.</p> <p>Coverslips with cells were mounted in the Chamlide chamber (Live Cell Instrument, Korea) and covered with imaging buffer (PBS pH 7.4, 50 mM MEA). Single-molecule localizations (SMLs) data were acquired by Zeiss Elyra PS.1 equipped with HR Diode 642-150 and HR DPSS 561-200 lasers, Alpha Plan-Apochromat 100x/1.46 oil DIC M27 Elyra objective and Andor EM CCD iXon DU 897 camera and Zeiss ZEN Black 2.1 SP3 software (Zeiss). AF647 and AF555 photo-switching was achieved by HiLo illumination and TIRF HP FOV with 100% power of 642nm or 561nm laser, and the signal was acquired via MBS 642 + EF LP 655 and MBS 561 + EF BP 570-620 / LP 750 filters, respectively. Exposure time was 40 ms and EM gain was 300 for both channels.</p> <p>SMLs were calculated in 2D by Zeiss ZEN Black 2.1 SP3 software using x,y 2D Gauss fit with point spread function (PSF) half width 177.9 nm, peak mask size 9 pixels and peak intensity to noise 6 and accounted for overlap in 2D with max cluster size 10. SMLs were rendered in ZEN software with 10 nm/px resolution and 1x PSF expansion factor. The data were model-based drift corrected in ZEN. Two channels were aligned using tetraspec beads fiducial markers for affine calibration. Drift-corrected and aligned localization coordinates were exported as text files. Text files were converted into csv files and imported using self-written macro (Hoboth et al., 2021a) into the ImageJ2 (Rueden et al., 2017) plug-in ThunderSTORM, visualized by normalized Gaussian method (Ovesny et al., 2014).</p>
Ditrect STORM imaging and image reconstruction of the transcription elongation marker P-S2 and nuclear PI(3,4)P2 indirectly immunolabeled with AF647 (red) and AF555 (green) in THZ1 treated cells.
<p>U-2 OS cells were grown in DMEM with 10% FBS at 37°C and 5% CO<sub>2</sub>. Cells were plated one day before staining in ~50% confluence on the high-precision 12 mm round coverslips treated with Hellmanex, sonicated, washed, dried and sterilized. Cells were treated for 3h with 1 µM THZ1 (MedChem HY80013) added to the culture media.</p> <p>U2OS cells were washed twice with PBS (pH 7.4) and fixed for 30 min in 2% PFA in PBS, washed 3-times for 5 min with PBS, then permeabilized in 0.1% Triton X-100 in PBS for 20 min, washed 3-times for 5 min by PBS and blocked in filtered 5% BSA in PBS for 30 min. Cells were incubated for 45 min with rabbit polyclonal IgG anti-RNAPII CTD P-S2 (Abcam ab5095) 3 µg/mL and mouse monoclonal IgG2 anti-PI(3,4)P2 (Z-P034; Echelon Biosci. Inc., USA) 5 µg/mL in 5% BSA in PBS, washed 3-times for 5 min in PBS and incubated for 30 min with donkey anti-mouse IgG AF555 (Invitrogen A31570) 10 µg/mL and goat anti-rabbit IgG AF647 (Invitrogen A21245) 10 µg/mL diluted in 5% BSA in PBS. Then the cells were washed 3-times for 5 min in PBS, post-fixed for 15 min in 2% PFA in PBS and washed 3-times for 5 min in PBS. All procedures were performed at RT and the cells were stored in PBS in the fridge overnight prior imaging.</p> <p>Coverslips with cells were mounted in the Chamlide chamber (Live Cell Instrument, Korea) and covered with imaging buffer (PBS pH 7.4, 50 mM MEA). Single-molecule localizations (SMLs) data were acquired by Zeiss Elyra PS.1 equipped with HR Diode 642-150 and HR DPSS 561-200 lasers, Alpha Plan-Apochromat 100x/1.46 oil DIC M27 Elyra objective and Andor EM CCD iXon DU 897 camera and Zeiss ZEN Black 2.1 SP3 software (Zeiss). AF647 and AF555 photo-switching was achieved by HiLo illumination and TIRF HP FOV with 100% power of 642nm or 561nm laser, and the signal was acquired via MBS 642 + EF LP 655 and MBS 561 + EF BP 570-620 / LP 750 filters, respectively. Exposure time was 40 ms and EM gain was 300 for both channels.</p> <p>SMLs were calculated in 2D by Zeiss ZEN Black 2.1 SP3 software using x,y 2D Gauss fit with point spread function (PSF) half width 177.9 nm, peak mask size 9 pixels and peak intensity to noise 6 and accounted for overlap in 2D with max cluster size 10. SMLs were rendered in ZEN software with 10 nm/px resolution and 1x PSF expansion factor. The data were model-based drift corrected in ZEN. Two channels were aligned using tetraspec beads fiducial markers for affine calibration. Drift-corrected and aligned localization coordinates were exported as text files. Text files were converted into csv files and imported using self-written macro (Hoboth et al., 2021a) into the ImageJ2 (Rueden et al., 2017) plug-in ThunderSTORM, visualized by normalized Gaussian method (Ovesny et al., 2014).</p>
Ditrect STORM imaging and image reconstruction of the transcription elongation marker P-S2 and nuclear PI(3,4)P2 indirectly immunolabeled with AF647 (red) and AF555 (green) in control cells.
<p>U-2 OS cells were grown in DMEM with 10% FBS at 37°C and 5% CO<sub>2</sub>. Cells were plated one day before staining in ~50% confluence on the high-precision 12 mm round coverslips treated with Hellmanex, sonicated, washed, dried and sterilized. Cells were control treated with 1:000 DMSO in the culture media.</p> <p>U2OS cells were washed twice with PBS (pH 7.4) and fixed for 30 min in 2% PFA in PBS, washed 3-times for 5 min with PBS, then permeabilized in 0.1% Triton X-100 in PBS for 20 min, washed 3-times for 5 min by PBS and blocked in filtered 5% BSA in PBS for 30 min. Cells were incubated for 45 min with rabbit polyclonal IgG anti-RNAPII CTD P-S2 (Abcam ab5095) 3 µg/mL and mouse monoclonal IgG2 anti-PI(3,4)P2 (Z-P034; Echelon Biosci. Inc., USA) 5 µg/mL in 5% BSA in PBS, washed 3-times for 5 min in PBS and incubated for 30 min with donkey anti-mouse IgG AF555 (Invitrogen A31570) 10 µg/mL and goat anti-rabbit IgG AF647 (Invitrogen A21245) 10 µg/mL diluted in 5% BSA in PBS. Then the cells were washed 3-times for 5 min in PBS, post-fixed for 15 min in 2% PFA in PBS and washed 3-times for 5 min in PBS. All procedures were performed at RT and the cells were stored in PBS in the fridge overnight prior imaging.</p> <p>Coverslips with cells were mounted in the Chamlide chamber (Live Cell Instrument, Korea) and covered with imaging buffer (PBS pH 7.4, 50 mM MEA). Single-molecule localizations (SMLs) data were acquired by Zeiss Elyra PS.1 equipped with HR Diode 642-150 and HR DPSS 561-200 lasers, Alpha Plan-Apochromat 100x/1.46 oil DIC M27 Elyra objective and Andor EM CCD iXon DU 897 camera and Zeiss ZEN Black 2.1 SP3 software (Zeiss). AF647 and AF555 photo-switching was achieved by HiLo illumination and TIRF HP FOV with 100% power of 642nm or 561nm laser, and the signal was acquired via MBS 642 + EF LP 655 and MBS 561 + EF BP 570-620 / LP 750 filters, respectively. Exposure time was 40 ms and EM gain was 300 for both channels.</p> <p>SMLs were calculated in 2D by Zeiss ZEN Black 2.1 SP3 software using x,y 2D Gauss fit with point spread function (PSF) half width 177.9 nm, peak mask size 9 pixels and peak intensity to noise 6 and accounted for overlap in 2D with max cluster size 10. SMLs were rendered in ZEN software with 10 nm/px resolution and 1x PSF expansion factor. The data were model-based drift corrected in ZEN. Two channels were aligned using tetraspec beads fiducial markers for affine calibration. Drift-corrected and aligned localization coordinates were exported as text files. Text files were converted into csv files and imported using self-written macro (Hoboth et al., 2021a) into the ImageJ2 (Rueden et al., 2017) plug-in ThunderSTORM, visualized by normalized Gaussian method (Ovesny et al., 2014).</p>
Ditrect STORM imaging and image reconstruction of the transcription initiation marker P-S2 and nuclear PI(3,4)P2 indirectly immunolabeled with AF647 (red) and AF555 (green) in DRB treated cells.
<p>U-2 OS cells were grown in DMEM with 10% FBS at 37°C and 5% CO<sub>2</sub>. Cells were plated one day before staining in ~50% confluence on the high-precision 12 mm round coverslips treated with Hellmanex, sonicated, washed, dried and sterilized. Cells were treated for 2h with 100 µM DRB (Sigma D1916) added to the cell culture media.</p> <p>U2OS cells were washed twice with PBS (pH 7.4) and fixed for 30 min in 2% PFA in PBS, washed 3-times for 5 min with PBS, then permeabilized in 0.1% Triton X-100 in PBS for 20 min, washed 3-times for 5 min by PBS and blocked in filtered 5% BSA in PBS for 30 min. Cells were incubated for 45 min with rabbit polyclonal IgG anti-RNAPII CTD P-S2 (Abcam ab5095) 3 µg/mL and mouse monoclonal IgG2 anti-PI(3,4)P2 (Z-P034; Echelon Biosci. Inc., USA) 5 µg/mL in 5% BSA in PBS, washed 3-times for 5 min in PBS and incubated for 30 min with donkey anti-mouse IgG AF555 (Invitrogen A31570) 10 µg/mL and goat anti-rabbit IgG AF647 (Invitrogen A21245) 10 µg/mL diluted in 5% BSA in PBS. Then the cells were washed 3-times for 5 min in PBS, post-fixed for 15 min in 2% PFA in PBS and washed 3-times for 5 min in PBS. All procedures were performed at RT and the cells were stored in PBS in the fridge overnight prior imaging.</p> <p>Coverslips with cells were mounted in the Chamlide chamber (Live Cell Instrument, Korea) and covered with imaging buffer (PBS pH 7.4, 50 mM MEA). Single-molecule localizations (SMLs) data were acquired by Zeiss Elyra PS.1 equipped with HR Diode 642-150 and HR DPSS 561-200 lasers, Alpha Plan-Apochromat 100x/1.46 oil DIC M27 Elyra objective and Andor EM CCD iXon DU 897 camera and Zeiss ZEN Black 2.1 SP3 software (Zeiss). AF647 and AF555 photo-switching was achieved by HiLo illumination and TIRF HP FOV with 100% power of 642nm or 561nm laser, and the signal was acquired via MBS 642 + EF LP 655 and MBS 561 + EF BP 570-620 / LP 750 filters, respectively. Exposure time was 40 ms and EM gain was 300 for both channels.</p> <p>SMLs were calculated in 2D by Zeiss ZEN Black 2.1 SP3 software using x,y 2D Gauss fit with point spread function (PSF) half width 177.9 nm, peak mask size 9 pixels and peak intensity to noise 6 and accounted for overlap in 2D with max cluster size 10. SMLs were rendered in ZEN software with 10 nm/px resolution and 1x PSF expansion factor. The data were model-based drift corrected in ZEN. Two channels were aligned using tetraspec beads fiducial markers for affine calibration. Drift-corrected and aligned localization coordinates were exported as text files. Text files were converted into csv files and imported using self-written macro (Hoboth et al., 2021a) into the ImageJ2 (Rueden et al., 2017) plug-in ThunderSTORM, visualized by normalized Gaussian method (Ovesny et al., 2014).</p>
Ditrect STORM imaging and image reconstruction of the transcription initiation marker P-S5 and nuclear PI(4,5)P2 indirectly immunolabeled with AF647 (red) and AF555 (green) in THZ1 treated cells.
<p>U-2 OS cells were grown in DMEM with 10% FBS at 37°C and 5% CO<sub>2</sub>. Cells were plated one day before staining in ~50% confluence on the high-precision 12 mm round coverslips treated with Hellmanex, sonicated, washed, dried and sterilized. Cells were treated for 3h with 1 µM THZ1 (MedChem HY80013) added to the culture media.</p> <p>U2OS cells were washed twice with PBS (pH 7.4) and fixed for 30 min in 2% PFA in PBS, washed 3-times for 5 min with PBS, then permeabilized in 0.1% Triton X-100 in PBS for 20 min, washed 3-times for 5 min by PBS and blocked in filtered 5% BSA in PBS for 30 min. Cells were incubated for 45 min with rabbit polyclonal IgG anti-RNAPII CTD P-S5 (Abcam ab5131) 3 µg/mL and mouse ascites IgM anti-PI(4,5)P2 2C11 (Z-A045; Echelon Biosci. Inc., USA) 5 µg/mL in 5% BSA in PBS, washed 3-times for 5 min in PBS and incubated for 30 min with goat anti-mouse IgM (µ-chain) AF555 (Jackson ImmunoRes. A24126) 10 µg/mL; goat anti-rabbit IgG AF647 (Invitrogen A21245) 10 µg/mL diluted in 5% BSA in PBS. Then the cells were washed 3-times for 5 min in PBS, post-fixed for 15 min in 2% PFA in PBS and washed 3-times for 5 min in PBS. All procedures were performed at RT and the cells were stored in PBS in the fridge overnight prior imaging.</p> <p>Coverslips with cells were mounted in the Chamlide chamber (Live Cell Instrument, Korea) and covered with imaging buffer (PBS pH 7.4, 50 mM MEA). Single-molecule localizations (SMLs) data were acquired by Zeiss Elyra PS.1 equipped with HR Diode 642-150 and HR DPSS 561-200 lasers, Alpha Plan-Apochromat 100x/1.46 oil DIC M27 Elyra objective and Andor EM CCD iXon DU 897 camera and Zeiss ZEN Black 2.1 SP3 software (Zeiss). AF647 and AF555 photo-switching was achieved by HiLo illumination and TIRF HP FOV with 100% power of 642nm or 561nm laser, and the signal was acquired via MBS 642 + EF LP 655 and MBS 561 + EF BP 570-620 / LP 750 filters, respectively. Exposure time was 40 ms and EM gain was 300 for both channels.</p> <p>SMLs were calculated in 2D by Zeiss ZEN Black 2.1 SP3 software using x,y 2D Gauss fit with point spread function (PSF) half width 177.9 nm, peak mask size 9 pixels and peak intensity to noise 6 and accounted for overlap in 2D with max cluster size 10. SMLs were rendered in ZEN software with 10 nm/px resolution and 1x PSF expansion factor. The data were model-based drift corrected in ZEN. Two channels were aligned using tetraspec beads fiducial markers for affine calibration. Drift-corrected and aligned localization coordinates were exported as text files. Text files were converted into csv files and imported using self-written macro (Hoboth et al., 2021a) into the ImageJ2 (Rueden et al., 2017) plug-in ThunderSTORM, visualized by normalized Gaussian method (Ovesny et al., 2014).</p>
Ditrect STORM imaging and image reconstruction of the transcription initiation marker P-S5 and nuclear PI(3,4)P2 indirectly immunolabeled with AF647 (red) and AF555 (green) in THZ1 treated cells.
<p>U-2 OS cells were grown in DMEM with 10% FBS at 37°C and 5% CO<sub>2</sub>. Cells were plated one day before staining in ~50% confluence on the high-precision 12 mm round coverslips treated with Hellmanex, sonicated, washed, dried and sterilized. Cells were treated for 3h with 1 µM THZ1 (MedChem HY80013) added to the culture media.</p> <p>U2OS cells were washed twice with PBS (pH 7.4) and fixed for 30 min in 2% PFA in PBS, washed 3-times for 5 min with PBS, then permeabilized in 0.1% Triton X-100 in PBS for 20 min, washed 3-times for 5 min by PBS and blocked in filtered 5% BSA in PBS for 30 min. Cells were incubated for 45 min with rabbit polyclonal IgG anti-RNAPII CTD P-S5 (Abcam ab5131) 3 µg/mL and mouse monoclonal IgG2 anti-PI(3,4)P2 (Z-P034; Echelon Biosci. Inc., USA) 5 µg/mL in 5% BSA in PBS, washed 3-times for 5 min in PBS and incubated for 30 min with donkey anti-mouse IgG AF555 (Invitrogen A31570) 10 µg/mL and goat anti-rabbit IgG AF647 (Invitrogen A21245) 10 µg/mL diluted in 5% BSA in PBS. Then the cells were washed 3-times for 5 min in PBS, post-fixed for 15 min in 2% PFA in PBS and washed 3-times for 5 min in PBS. All procedures were performed at RT and the cells were stored in PBS in the fridge overnight prior imaging.</p> <p>Coverslips with cells were mounted in the Chamlide chamber (Live Cell Instrument, Korea) and covered with imaging buffer (PBS pH 7.4, 50 mM MEA). Single-molecule localizations (SMLs) data were acquired by Zeiss Elyra PS.1 equipped with HR Diode 642-150 and HR DPSS 561-200 lasers, Alpha Plan-Apochromat 100x/1.46 oil DIC M27 Elyra objective and Andor EM CCD iXon DU 897 camera and Zeiss ZEN Black 2.1 SP3 software (Zeiss). AF647 and AF555 photo-switching was achieved by HiLo illumination and TIRF HP FOV with 100% power of 642nm or 561nm laser, and the signal was acquired via MBS 642 + EF LP 655 and MBS 561 + EF BP 570-620 / LP 750 filters, respectively. Exposure time was 40 ms and EM gain was 300 for both channels.</p> <p>SMLs were calculated in 2D by Zeiss ZEN Black 2.1 SP3 software using x,y 2D Gauss fit with point spread function (PSF) half width 177.9 nm, peak mask size 9 pixels and peak intensity to noise 6 and accounted for overlap in 2D with max cluster size 10. SMLs were rendered in ZEN software with 10 nm/px resolution and 1x PSF expansion factor. The data were model-based drift corrected in ZEN. Two channels were aligned using tetraspec beads fiducial markers for affine calibration. Drift-corrected and aligned localization coordinates were exported as text files. Text files were converted into csv files and imported using self-written macro (Hoboth et al., 2021a) into the ImageJ2 (Rueden et al., 2017) plug-in ThunderSTORM, visualized by normalized Gaussian method (Ovesny et al., 2014).</p>
Ditrect STORM imaging and image reconstruction of the transcription initiation marker P-S5 and nuclear PI(3,4)P2 indirectly immunolabeled with AF647 (red) and AF555 (green) in DRB treated cells.
<p>U-2 OS cells were grown in DMEM with 10% FBS at 37°C and 5% CO<sub>2</sub>. Cells were plated one day before staining in ~50% confluence on the high-precision 12 mm round coverslips treated with Hellmanex, sonicated, washed, dried and sterilized. Cells were treated for 2h with 100 µM DRB (Sigma D1916) added to the cell culture media.</p> <p>U2OS cells were washed twice with PBS (pH 7.4) and fixed for 30 min in 2% PFA in PBS, washed 3-times for 5 min with PBS, then permeabilized in 0.1% Triton X-100 in PBS for 20 min, washed 3-times for 5 min by PBS and blocked in filtered 5% BSA in PBS for 30 min. Cells were incubated for 45 min with rabbit polyclonal IgG anti-RNAPII CTD P-S5 (Abcam ab5131) 3 µg/mL and mouse monoclonal IgG2 anti-PI(3,4)P2 (Z-P034; Echelon Biosci. Inc., USA) 5 µg/mL in 5% BSA in PBS, washed 3-times for 5 min in PBS and incubated for 30 min with donkey anti-mouse IgG AF555 (Invitrogen A31570) 10 µg/mL and goat anti-rabbit IgG AF647 (Invitrogen A21245) 10 µg/mL diluted in 5% BSA in PBS. Then the cells were washed 3-times for 5 min in PBS, post-fixed for 15 min in 2% PFA in PBS and washed 3-times for 5 min in PBS. All procedures were performed at RT and the cells were stored in PBS in the fridge overnight prior imaging.</p> <p>Coverslips with cells were mounted in the Chamlide chamber (Live Cell Instrument, Korea) and covered with imaging buffer (PBS pH 7.4, 50 mM MEA). Single-molecule localizations (SMLs) data were acquired by Zeiss Elyra PS.1 equipped with HR Diode 642-150 and HR DPSS 561-200 lasers, Alpha Plan-Apochromat 100x/1.46 oil DIC M27 Elyra objective and Andor EM CCD iXon DU 897 camera and Zeiss ZEN Black 2.1 SP3 software (Zeiss). AF647 and AF555 photo-switching was achieved by HiLo illumination and TIRF HP FOV with 100% power of 642nm or 561nm laser, and the signal was acquired via MBS 642 + EF LP 655 and MBS 561 + EF BP 570-620 / LP 750 filters, respectively. Exposure time was 40 ms and EM gain was 300 for both channels.</p> <p>SMLs were calculated in 2D by Zeiss ZEN Black 2.1 SP3 software using x,y 2D Gauss fit with point spread function (PSF) half width 177.9 nm, peak mask size 9 pixels and peak intensity to noise 6 and accounted for overlap in 2D with max cluster size 10. SMLs were rendered in ZEN software with 10 nm/px resolution and 1x PSF expansion factor. The data were model-based drift corrected in ZEN. Two channels were aligned using tetraspec beads fiducial markers for affine calibration. Drift-corrected and aligned localization coordinates were exported as text files. Text files were converted into csv files and imported using self-written macro (Hoboth et al., 2021a) into the ImageJ2 (Rueden et al., 2017) plug-in ThunderSTORM, visualized by normalized Gaussian method (Ovesny et al., 2014).</p>
Ditrect STORM imaging and image reconstruction of the transcription elongation marker P-S2 and nuclear PI(4,5)P2 indirectly immunolabeled with AF647 (red) and AF555 (green) in control cells.
<p>U-2 OS cells were grown in DMEM with 10% FBS at 37°C and 5% CO<sub>2</sub>. Cells were plated one day before staining in ~50% confluence on the high-precision 12 mm round coverslips treated with Hellmanex, sonicated, washed, dried and sterilized. Cells were control treated with 1:000 DMSO in the culture media.</p> <p>U2OS cells were washed twice with PBS (pH 7.4) and fixed for 30 min in 2% PFA in PBS, washed 3-times for 5 min with PBS, then permeabilized in 0.1% Triton X-100 in PBS for 20 min, washed 3-times for 5 min by PBS and blocked in filtered 5% BSA in PBS for 30 min. Cells were incubated for 45 min with rabbit polyclonal IgG anti-RNAPII CTD P-S2 (Abcam ab5095) 3 µg/mL and mouse ascites IgM anti-PI(4,5)P2 2C11 (Z-A045; Echelon Biosci. Inc., USA) 5 µg/mL in 5% BSA in PBS, washed 3-times for 5 min in PBS and incubated for 30 min with goat anti-mouse IgM (µ-chain) AF555 (Jackson ImmunoRes. A24126) 10 µg/mL; goat anti-rabbit IgG AF647 (Invitrogen A21245) 10 µg/mL diluted in 5% BSA in PBS. Then the cells were washed 3-times for 5 min in PBS, post-fixed for 15 min in 2% PFA in PBS and washed 3-times for 5 min in PBS. All procedures were performed at RT and the cells were stored in PBS in the fridge overnight prior imaging.</p> <p>Coverslips with cells were mounted in the Chamlide chamber (Live Cell Instrument, Korea) and covered with imaging buffer (PBS pH 7.4, 50 mM MEA). Single-molecule localizations (SMLs) data were acquired by Zeiss Elyra PS.1 equipped with HR Diode 642-150 and HR DPSS 561-200 lasers, Alpha Plan-Apochromat 100x/1.46 oil DIC M27 Elyra objective and Andor EM CCD iXon DU 897 camera and Zeiss ZEN Black 2.1 SP3 software (Zeiss). AF647 and AF555 photo-switching was achieved by HiLo illumination and TIRF HP FOV with 100% power of 642nm or 561nm laser, and the signal was acquired via MBS 642 + EF LP 655 and MBS 561 + EF BP 570-620 / LP 750 filters, respectively. Exposure time was 40 ms and EM gain was 300 for both channels.</p> <p>SMLs were calculated in 2D by Zeiss ZEN Black 2.1 SP3 software using x,y 2D Gauss fit with point spread function (PSF) half width 177.9 nm, peak mask size 9 pixels and peak intensity to noise 6 and accounted for overlap in 2D with max cluster size 10. SMLs were rendered in ZEN software with 10 nm/px resolution and 1x PSF expansion factor. The data were model-based drift corrected in ZEN. Two channels were aligned using tetraspec beads fiducial markers for affine calibration. Drift-corrected and aligned localization coordinates were exported as text files. Text files were converted into csv files and imported using self-written macro (Hoboth et al., 2021a) into the ImageJ2 (Rueden et al., 2017) plug-in ThunderSTORM, visualized by normalized Gaussian method (Ovesny et al., 2014).</p>
Ditrect STORM imaging and image reconstruction of the transcription elongation marker P-S2 and nuclear PI(4,5)P2 indirectly immunolabeled with AF647 (red) and AF555 (green) in DRB treated cells.
<p>U-2 OS cells were grown in DMEM with 10% FBS at 37°C and 5% CO<sub>2</sub>. Cells were plated one day before staining in ~50% confluence on the high-precision 12 mm round coverslips treated with Hellmanex, sonicated, washed, dried and sterilized. Cells were treated for 2h with 100 µM DRB (Sigma D1916) added to the cell culture media.</p> <p>U2OS cells were washed twice with PBS (pH 7.4) and fixed for 30 min in 2% PFA in PBS, washed 3-times for 5 min with PBS, then permeabilized in 0.1% Triton X-100 in PBS for 20 min, washed 3-times for 5 min by PBS and blocked in filtered 5% BSA in PBS for 30 min. Cells were incubated for 45 min with rabbit polyclonal IgG anti-RNAPII CTD P-S2 (Abcam ab5095) 3 µg/mL and mouse ascites IgM anti-PI(4,5)P2 2C11 (Z-A045; Echelon Biosci. Inc., USA) 5 µg/mL in 5% BSA in PBS, washed 3-times for 5 min in PBS and incubated for 30 min with goat anti-mouse IgM (µ-chain) AF555 (Jackson ImmunoRes. A24126) 10 µg/mL; goat anti-rabbit IgG AF647 (Invitrogen A21245) 10 µg/mL diluted in 5% BSA in PBS. Then the cells were washed 3-times for 5 min in PBS, post-fixed for 15 min in 2% PFA in PBS and washed 3-times for 5 min in PBS. All procedures were performed at RT and the cells were stored in PBS in the fridge overnight prior imaging.</p> <p>Coverslips with cells were mounted in the Chamlide chamber (Live Cell Instrument, Korea) and covered with imaging buffer (PBS pH 7.4, 50 mM MEA). Single-molecule localizations (SMLs) data were acquired by Zeiss Elyra PS.1 equipped with HR Diode 642-150 and HR DPSS 561-200 lasers, Alpha Plan-Apochromat 100x/1.46 oil DIC M27 Elyra objective and Andor EM CCD iXon DU 897 camera and Zeiss ZEN Black 2.1 SP3 software (Zeiss). AF647 and AF555 photo-switching was achieved by HiLo illumination and TIRF HP FOV with 100% power of 642nm or 561nm laser, and the signal was acquired via MBS 642 + EF LP 655 and MBS 561 + EF BP 570-620 / LP 750 filters, respectively. Exposure time was 40 ms and EM gain was 300 for both channels.</p> <p>SMLs were calculated in 2D by Zeiss ZEN Black 2.1 SP3 software using x,y 2D Gauss fit with point spread function (PSF) half width 177.9 nm, peak mask size 9 pixels and peak intensity to noise 6 and accounted for overlap in 2D with max cluster size 10. SMLs were rendered in ZEN software with 10 nm/px resolution and 1x PSF expansion factor. The data were model-based drift corrected in ZEN. Two channels were aligned using tetraspec beads fiducial markers for affine calibration. Drift-corrected and aligned localization coordinates were exported as text files. Text files were converted into csv files and imported using self-written macro (Hoboth et al., 2021a) into the ImageJ2 (Rueden et al., 2017) plug-in ThunderSTORM, visualized by normalized Gaussian method (Ovesny et al., 2014).</p>
Ditrect STORM imaging and image reconstruction of the transcription initiation marker P-S5 and nuclear PI(3,4)P2 indirectly immunolabeled with AF647 (red) and AF555 (green) in control cells.
<p>U-2 OS cells were grown in DMEM with 10% FBS at 37°C and 5% CO<sub>2</sub>. Cells were plated one day before staining in ~50% confluence on the high-precision 12 mm round coverslips treated with Hellmanex, sonicated, washed, dried and sterilized. Cells were control treated with 1:000 DMSO in the culture media.</p> <p>U2OS cells were washed twice with PBS (pH 7.4) and fixed for 30 min in 2% PFA in PBS, washed 3-times for 5 min with PBS, then permeabilized in 0.1% Triton X-100 in PBS for 20 min, washed 3-times for 5 min by PBS and blocked in filtered 5% BSA in PBS for 30 min. Cells were incubated for 45 min with rabbit polyclonal IgG anti-RNAPII CTD P-S5 (Abcam ab5131) 3 µg/mL and mouse monoclonal IgG2 anti-PI(3,4)P2 (Z-P034; Echelon Biosci. Inc., USA) 5 µg/mL in 5% BSA in PBS, washed 3-times for 5 min in PBS and incubated for 30 min with donkey anti-mouse IgG AF555 (Invitrogen A31570) 10 µg/mL and goat anti-rabbit IgG AF647 (Invitrogen A21245) 10 µg/mL diluted in 5% BSA in PBS. Then the cells were washed 3-times for 5 min in PBS, post-fixed for 15 min in 2% PFA in PBS and washed 3-times for 5 min in PBS. All procedures were performed at RT and the cells were stored in PBS in the fridge overnight prior imaging.</p> <p>Coverslips with cells were mounted in the Chamlide chamber (Live Cell Instrument, Korea) and covered with imaging buffer (PBS pH 7.4, 50 mM MEA). Single-molecule localizations (SMLs) data were acquired by Zeiss Elyra PS.1 equipped with HR Diode 642-150 and HR DPSS 561-200 lasers, Alpha Plan-Apochromat 100x/1.46 oil DIC M27 Elyra objective and Andor EM CCD iXon DU 897 camera and Zeiss ZEN Black 2.1 SP3 software (Zeiss). AF647 and AF555 photo-switching was achieved by HiLo illumination and TIRF HP FOV with 100% power of 642nm or 561nm laser, and the signal was acquired via MBS 642 + EF LP 655 and MBS 561 + EF BP 570-620 / LP 750 filters, respectively. Exposure time was 40 ms and EM gain was 300 for both channels.</p> <p>SMLs were calculated in 2D by Zeiss ZEN Black 2.1 SP3 software using x,y 2D Gauss fit with point spread function (PSF) half width 177.9 nm, peak mask size 9 pixels and peak intensity to noise 6 and accounted for overlap in 2D with max cluster size 10. SMLs were rendered in ZEN software with 10 nm/px resolution and 1x PSF expansion factor. The data were model-based drift corrected in ZEN. Two channels were aligned using tetraspec beads fiducial markers for affine calibration. Drift-corrected and aligned localization coordinates were exported as text files. Text files were converted into csv files and imported using self-written macro (Hoboth et al., 2021a) into the ImageJ2 (Rueden et al., 2017) plug-in ThunderSTORM, visualized by normalized Gaussian method (Ovesny et al., 2014).</p>
Donor Age and Red Cell Age Contribute to the Variance in Lorrca Indices in Healthy Donors for Next Generation Ektacytometry: A Pilot Study
<p>This dataset refers to the article "Donor Age and Red Cell Age Contribute to the Variance in Lorrca Indices in Healthy Donors for Next Generation Ektacytometry: A Pilot Study" Front. Physiol. 12:639722 2021</p> <p>DOI: 10.3389/fphys.2021.639722</p>
Terminal density reversal and the role of Ca2+ in red blood cells clearance of healthy individuals
<p>Density reversal of senescent red blood cells (RBCs) has been known for more than ten years, yet the identity of the candidate protein(s) is still elusive. While performing Percoll density gradient separation of RBCs from healthy individuals and their subsequent characterization, we identified a fraction of cells in the low-density fraction (~0.025% compared to total RBCs population) which shows reversal in their densities along with the characteristics of cellular senescence such as loss of membrane Band 3 protein and the phosphatidylserine exposure to the outer membrane leaflet. Our subsequent analysis showed that these cells are overloaded with Ca<sup>2+</sup>. We further measured intracellular [Na<sup>+</sup>] in individual RBCs by flow cytometry utilizing the dye CoroNa Green-AM. Our findings showed that the cells with senescent characteristics lost their transmembrane Na<sup>+</sup> gradient despite maintaining the membrane integrity. Consequently, these findings lead us to designate these cells as “senescent-like” cells. Our data further demonstrated altered activities of nonselective cation channels and pumps in these cells. In addition to a facilitated Na+ extrusion by Na<sup>+</sup>, K+-ATPase, our findings indicated altered ion transport via Piezo1 in these cells. Pharmacological modulation of Piezo1 with Yoda1/GsMTx4 showed that Piezo1 and, possibly, other nonselective cation channels by promiscuously transporting Na<sup>+</sup> and Ca<sup>2+</sup> play an important role in producing these low density “senescent like” cells.</p>
Fig. 1 in Histological, Topographical And Ultrastructural Organization Of Different Cells Lining The Olfactory Epithelium Of Red Piranha, Pygocentrus Nattereri (Characiformes, Serrasalmidae)
Fig. 1. Photomicrographs of the olfactory epithelium of Pygocentrus nattereri by scanning electron microscopy (SEM) and histological architecture stained with Delafield's Haematoxylin-Eosin (HE) and Mallory's triple (MT) stain. A — oval shaped olfactory rosette showing olfactory lamellae (OL) radiating from median raphe (R). Note tongue shaped structure (arrow heads) on the apical end of the lamellae (SEM) ×50. B — sensory olfactory epithelium (OEP) lined with receptor cells. Note the presence of blood vessels (BV) in the central core (CC) which is distinguished from OEP by basement membrane (BM). Arrow heads indicate basal cells above BM (MT) ×400. C — higher magnification of OEP showing a large number of primary receptor cells (RC) with conspicuous nuclei (N), secondary recptor cells (broken arrows), microvillous cells (MV) intermingled with supporting cells (SC). Note the presence of BV in CC and BC (arrow heads) near CC. Solid arrow indicates the axons of secondary RC communicate to CC (MT) ×1000. D — OEP exhibiting cylindrical RC with knob like vesicles (black arrow heads), ciliated supporting cells (solid arrows), non-ciliated supporting cells (white arrow heads) and BC above CC. Broken arrows mark the cilia of supporting cells on the epithelial surface (HE) ×400. E — tuft of receptor cells (RC) in between supporting cells (SC) (SEM) ×4000. F — dendrite patches of RC (broken arrows) and microvillous cells (solid arrows) in between stratified epithelial cells (SEC). Note the opening of mucous cells (arrow heads) in between SEC (SEM) ×2500.
Fig. 2 in Histological, Topographical And Ultrastructural Organization Of Different Cells Lining The Olfactory Epithelium Of Red Piranha, Pygocentrus Nattereri (Characiformes, Serrasalmidae)
Fig. 2. Photomicrographs of the olfactory epithelium of P. nattereri by scanning electron microscopy (SEM), transmission electron microscopy (TEM) and histological features stained with Mallory's triple (MT) stain. A — transitional zone between sensory epithelium (SE) with receptor cells (solid arrows) and non-sensory epithelium (NSE) having a series of mucous cells (MC) (Broken arrows), labyrinth cells (LC) and stratified epithelial cells (arrow heads). Olfactory epithelium separated from central core (CC) by a basement membrane (BM) (MT) ×400. B — surface of non-sensory epithelium showing densely arranged ciliated supporting cells (solid arrows) encircled the non-ciliated supporting cells (SC) with adhering mucin mass (arrow heads). Note the opening of MC (broken arrows) in between SC (SEM) ×4500. C — dendrite of receptor cell (RC) emerging out from basal body (broken arrow). Note microtubules of rod (solid arrow) parallel arranged (TEM) ×5000. D —nuclei of receptor cells (N) showing dispersed heterochromatin (arrow heads). Note the presence of mitochondria (solid arrows) adjacent to nucleus (TEM) ×500. (E) Showing cisterns of rough endoplasmic reticulum (rER) (arrow heads) encircling nucleus (solid arrow). Note Golgi apparatus (broken arrow) adjacent to rER (TEM) ×4000. F — OEP lined with microvillous cells (MV), mucous cell (MC) and supporting cell (broken arrow) (TEM) ×2100. G — microvillous cells exhibiting abundant ribosomes (broken arrows) and extended mitochondria (arrow heads). Solid arrow indicates nucleus (TEM) ×5000. H — axons (broken arrows) of receptor cells run parallel on both sides of basal cells (solid arrow) (TEM) ×5000.
Fig. 3 in Histological, Topographical And Ultrastructural Organization Of Different Cells Lining The Olfactory Epithelium Of Red Piranha, Pygocentrus Nattereri (Characiformes, Serrasalmidae)
Fig. 3. Photomicrographs of the olfactory epithelium of P. nattereri by transmission electron microscopy (TEM) and scanning electron microscopy (SEM). A — olfactory epithelium (OEP showing mucous cell (MC) having granules, microvillous cell (arrow head), labyrinth cell (broken arrow) and vesicular cytoplasm of supporting cell (solid arrow) (TEM) ×2100. B — flat surface ciliated supporting cell (solid arrow) provided with plenty of kinocilia (arrow heads) showing microtubular pattern (broken arrows). Note large number of mitochondria within the cytoplasm of supporting cells (TEM) ×5000. C — non-sensory olfactory epithelium (OEP) comprised of MC filled with large granules and supporting cells (solid arrows) (TEM) ×2100. D — basal cells provided with conspicuous lobular nuclei (N) having dense nucleolus (solid arrow). Note the presence of small vesicles (arrow head) adjacent the nucleus and rough endoplasmic reticulum (rER) (broken arrows) (TEM) ×2500. E — showing nuclear division of basal cells provided with dense nucleus (solid arrows). Broken arrows indicate mature nucleus of basal cells (TEM) ×2500. F — showing labyrinth cells (solid arrow) with conspicuous folding encircled by compactly arranged stratified epithelial cells (SEC). Note the presence of MC (broken arrows) in between SEC and mucin droplets (arrow heads) over SEC (SEM) ×4500. G — surface epithelium of raphe provided with packed SEC having labyrinth pattern microridges. Note the presence of opening of MC (solid arrows) and mucin droplets (arrow heads) over SEC (SEM) ×4500. H — raphe showing oval and elongated nuclei (N) of Stratified epithelial cells. Note the presence of rER (solid arrows) and vesicles (broken arrows) adjacent to nucleus (TEM) × 2500.
The protein organization of a red blood cell
<p>Elution profiles, feature matrix, train and test ppis, and metadata for the paper "The protein organization of a red blood cell". Sae-Lee et al., </p>
Figure 2 in Oxidative and osmotolerant effects in Salvator merianae (Squamata: Teiidae) red blood cells during hibernation
Figure 2. Logarithmic in base 10 values of oxidative biomolecules level for each period collected (n = 6). Wilcox Test: P = 0.31. Sum symbol (+) is the mean and SD are the horizontal lines; median is the vertical line within the boxes and range is distance from the median to the end of the boxes.
Figure 1 in Oxidative and osmotolerant effects in Salvator merianae (Squamata: Teiidae) red blood cells during hibernation
Figure 1. (a) Osmotic fragility in percentage by saline concentration from both periods studied (GLM: F = 2.56, P = 0.03). No statistical differences were observed between individualized pairs of saline concentrations; (b) Overall osmotic fragility difference between periods considering only periods effect (GLM: F = 9.72, P = 0.01) (n = 6). Sum symbol (+) is the mean and SD are the horizontal lines; median is the vertical line within the boxes and range is distance from the median to the end of the boxes.
Figure 3 in Oxidative and osmotolerant effects in Salvator merianae (Squamata: Teiidae) red blood cells during hibernation
Figure 3. Logarithmic in base 10 values of (a) Enzymatic activity level of glutathione peroxidase – GPx and (b) activity of glutathione reductase - GR of red blood cells in hibernation and active periods (n = 6). T-test, P = 0.68 and P = 0.10, respectively. Sum symbol (+) is the mean and SD are the horizontal lines; median is the vertical line within the boxes and range is distance from the median to the end of the boxes.
Time-averaged simulation results and in vivo measurements to show the impact of red blood cells on the flow field in the cortical microvasculature
<p>The dataset contains 5 files. 4 of them are time-averaged results of blood flow simulations with discrete red blood cell (RBC) tracking in realistic microvascular networks. The 5th file contains median values of RBC velocity measurements at capillary bifurcations in the somatosensory cortex of the mouse.</p> <p>Further notes on the simulation results:<br> - The realistic microvascular networks are from the mouse parietal cortex and have first been published in Blinder et al., 2013, Nature Neuroscience (<a href="https://doi.org/10.1038/nn.3426">https://doi.org/10.1038/nn.3426</a>).<br> - The numerical model to simulate blood flow in realistic microvascular networks has been described in Schmid et al., 2017, PLOS Computational Biology (<a href="https://doi.org/10.1371/journal.pcbi.1005392">https://doi.org/10.1371/journal.pcbi.1005392</a>).<br> - MVN1 and MVN2 stands for microvascular network 1 and 2, respectively.<br> - wRBCs and wpPs stands for 'with red blood cells' and 'with passive particles'. These terms describe two different numerical models: The wRBC-model accounts for all RBC related flow phenomena. The wpP neglects the phase-separation and the Fahraeus-Lindqvist effect, i.e. RBCs and flow are decoupled. Further details are available from Schmid et al. (2019, <a href="https://doi.org/10.1371/journal.pcbi.1007231">https://doi.org/10.1371/journal.pcbi.1007231</a>)</p> <p><strong>File format: </strong>pickle (Python)</p> <p><strong>Files 1 - 4 </strong>(Time-averaged simulation results):<br> Filenames: MVN1_wpPs.tar.bz2, MVN2_wpPs.tar.bz2, MVN1_wRBCs.tar.bz2, MVN2_wRBCs.tar.bz2</p> <p>Each compressed folder contains two files:<br> <br> edgesDict.pkl: dictionary with edge/vessel related data: </p> <ul> <li>flow: Flow rate in vessel [um^3/ms]</li> <li>length: Vessel length [um] (Tortuosity is considered)</li> <li>htt: Tube hematocrit in vessel [-]</li> <li>diameter: Effective vessel diameter [um]</li> <li>connectivity: Vertex indices, e.g. start and end vertex of the corresponding vessel</li> </ul> <p>verticesDict.pkl: dictionary with vertex/bifurcation related data:</p> <ul> <li>index: Index of the current vertex </li> <li>coords: Coordinates to describe the position of the vertex [um]</li> <li>pressure: Pressure at the vertex [mmHg]</li> </ul> <p> </p> <p><strong>File 5</strong> (in vivo RBC velocity measurements):<br> Filename: measurementDict.pkl</p> <p>keys:</p> <ul> <li>divergent_d1: divergent bifurcation, RBC velocity measurement in daughter vessel 1</li> <li>divergent_d2: divergent bifurcation, RBC velocity measurement in daughter vessel 2</li> <li>convergent_m1: convergent bifurcation, RBC velocity measurement in mother vessel 1</li> <li>convergent_m2: convergent bifurcation, RBC velocity measurement in mother vessel 2</li> </ul> <p><br> Data structure: list of list,<br> e.g. daughter vessel 1:<br> [[bif.1 - measure.1, bif.1 - measure.2, bif.1 - measure.3], [bif.2 - measure.1, bif.2 - measure.2, bif.2 - measure.3],...]<br> bif.: bifurcation, measure.: measurement.<br> The order of bifurcations is the same for 'divergent_d1' and 'divergent_d2' (and for 'convergent_m1' and 'convergent_m2'). </p> <p> </p>
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.