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5 results for “mtFociCounter”
Image data for bioRxiv article named: mtFociCounter - Reproducible, open source and quantitative single-cell analysis of mitochondrial nucleoids and other foci
<p>Raw imaging data to reproduce and test the findings of the bioRxiv article: <strong>mtFociCounter </strong>- Reproducible, open source and quantitative single-cell analysis of mitochondrial nucleoids and other foci. It contains data from three imaging days and 2 or three technical replicates on each day.</p> <p> </p>
Imaging dataset 01 for mtFociCounter
<p>This is the first dataset associated with the updated manuscript on mtFociCounter.</p> <p>Images are Spinning Disk Confocal Images of unsorted 3t3 NIH mouse fibroblasts stably expressing <strong>mitochondrially</strong> targeted dsRed, immunofluorescence against dsDNA (mitochondrial <strong>nucleoids</strong>) and AlexaFluor 647, and stained <strong>nuclei</strong> with Hoechst.</p> <p>It contains all data necessary to reproduce the analysis of 3t3 WT sampling (sample-to-sample comparison), as described in the manuscript. "samples" from the same day are 13mm coverslips processed in parallel (seeding of cells, fixation, immunofluorescence) and mounted on the same glass slide (#1 on left, #2 centre, #3 right). The dataset contains the 3t3 WT data from the following acquisition dates:</p> <p>20220603_sample2<br> 20220603_sample3<br> 20220706_sample2<br> 20220706_sample3<br> 20220708_sample1<br> 20220708_sample2<br> 20220708_sample3<br> 20221022_sample2<br> 20221022_sample3</p> <p>For details of the sampling procedure, please refer to the accompanying manuscript, which will soon be made available on BioRxiv.<br> </p>
Imaging dataset 03 for mtFociCounter
<p>This is the third dataset associated with the updated manuscript on <strong>mtFociCounter</strong>.</p> <p>Images are Spinning Disk Confocal Images of unsorted 3t3 NIH mouse fibroblasts stably expressing <strong>mitochondrially </strong>targeted dsRed, immunofluorescence against dsDNA (mitochondrial <strong>nucleoids</strong>) and AlexaFluor 647, and <strong>nuclei </strong>stained with Hoechst.</p> <p>Together with dataset_01, it contains all data necessary to reproduce the analysis of 3t3 WT cells, as described in the manuscript. "samples" from the same day are 13mm coverslips processed in parallel (seeding of cells, fixation, immunofluorescence and imaging) and mounted on the same glass slide (#1 on left, #2 centre, #3 right), whereas different dates can be considered biological replicates, of which there are 19 in total (with dataset 01).<br> Please <strong>beware</strong>, there is some redundancy with dataset_02, and we recommend <strong>combining dataset_01 with dataset_03 for further analysis</strong>. This dataset_03 contains the 3t3 WT data from the following acquisition dates:</p> <p>20221025_sample1<br> 20221026_sample2<br> 20221029_sample1<br> 20221029_sample2<br> 20221110_sample2<br> 20221210_sample1<br> 20221211_sample3<br> 20221212_sample3<br> 20221217_sample2<br> 20221220_sample2<br> 20221221_sample3</p> <p>For further details on the experimental procedure, please refer to the accompanying manuscript, which will soon be made available on BioRxiv.</p>
Imaging dataset 02 for mtFociCounter
<p>This is the second dataset associated with the updated manuscript on mtFociCounter.</p> <p>Images are Spinning Disk Confocal Images of unsorted 3t3 NIH mouse fibroblasts stably expressing <strong>mitochondrially </strong>targeted dsRed, immunofluorescence against dsDNA (mitochondrial <strong>nucleoids</strong>) and AlexaFluor 647, and stained <strong>nuclei </strong>with Hoechst.</p> <p>It contains all data necessary to reproduce the testing of mtFociCounter (no primary control; rho0 control; manual cell segmentation), as described in the manuscript. Samples were processed and imaged in parallel, on the same date, in biological replicates (different date). The dataset contains the 3t3 WT data from the following acquisition dates:</p> <p>no primary antibody (no1) vs. with primary antibody against dsDNA (nucleoids):<br> 20221022_no1 vs. wt<br> 20221025_no1 vs. wt<br> 20221029_no1 vs. wt</p> <p>for 3t3 cells depleted of mtDNA (rho0) vs. normal 3t3 cells with mtDNA (wt):<br> 20221223: sample_1 & sample_2 rho0 vs. sample_3 wt</p> <p>for 3t3 WT cells, same raw-data, manually segmented single cells on two independent days:<br> 20221022 -> segmentation on 20221102 vs. segmentation on 20221103<br> 20221029 -> segmentation on 20221102 vs. segmentation on 20221104</p> <p>For further details of the exact experimental procedure, please refer to the accompanying manuscript, which will soon be made available on BioRxiv.</p>
Imaging dataset 04 for mtFociCounter
<p>This is the fourth dataset associated with the updated manuscript on mtFociCounter.</p> <p>Images are Spinning Disk Confocal Images of unsorted U2OS cells treated with siRNA against TFAM (siTFAM) or neutral siRNA (siNT). Cells were stained with antibodies against tom20 (<strong>mitochondria</strong>) and against dsDNA (<strong>nucleoids</strong>).<br> The second folder contains SIM2 images acquired on an Elyra7 microscope of 3t3 wild-type fibroblasts, which express <strong>mitochondrially </strong>targeted dsRed, and are stained by immunofluorescence against dsDNA (<strong>nucleoids</strong>) and AlexaFluor 647, as well as Hoecst for <strong>nuclei</strong>.</p> <p>This repository contains all data necessary to reproduce the analysis of siTFAM and 3t3-superresolution, as described in the manuscript. The dataset contains the following data:</p> <p>U2OS treated with siTFAM or neutral (WT):<br> 20210212 siTFAM vs. siNT<br> 20210217 siTFAM vs. siNT<br> 20210222 siTFAM vs. siNT</p> <p>3t3 WT fibroblasts images by Elyra7 SIM2:<br> 20221221<br> 20230118<br> 20230120</p> <p><br> The third folder contains images from Spinning Disk Confocal Images of unsorted U2OS cells. Cells were stained with antibodies against tom20 (mitochondria) and against FASTKD2 (MRGs).<br> The fourth folder contains raw Western Blot and Coomassie staining images from unsorted U2OS cells treated with a neutral siRNA or an siRNA against TFAM for 3 days. Antibodies against tubulin, TFAM or pre-TFAM were used, as indicated.</p> <p>This repository contains all data necessary to reproduce the analysis of MRG numbers or TFAM knockdown assessment, as described in the manuscript.</p> <p>U2OS WT cells:<br> 20230429 FASTKD2<br> 20230505 FASTKD2<br> 20230505 FASTKD2<br> <br> For details of the experimental procedure, please refer to the accompanying manuscript, which will soon be made available on BioRxiv.</p>
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