Single-cell chromatin accessibility profiling reveals a self-renewing muscle satellite cell state

FigS3M_counting: Number of Fibers per microscopy field for SMAD4iKO muscle vs WT.
FigS3O_count: Fiber size in SMAD4 iKO muscle vs wildtype. The percentage of fibers in various size bins is also evaluated.
Figure4-raw-images: Immunostaining microscopy images of Betaglycan (purple), EdU (green), Pax7 (red) and DAPI (blue) in acutely injured muscle at 3 and 4.5 days post injury (4E). 4G: Similar immunostaining image for recipient mouse muscle following transplantation of lineage traced (GFP) muscle stem cells.
Fig_S3-raw-images: Immunostaining and H&E images of wildtype and SMAD4 iKO mouse muscle.
Figure6-raw-images: Immunostaining of cultured SMAD4 iKO and wildtype myoblasts with overexpression of Id1, Id2, and Id3 (I), and knockdown of Cdkn1c.
Figure_5_raw_images: Immunostaining images of WT and SMAD4 iKO muscle fibers (E and K) single (E) and repeated (K) acute injuries. In vivo immunostaining images of muscle tissue from similar conditions (G and M).
Fig5H_CTX30D_section_Pax7.xlsx: Quantification of Pax7-expressing cells in in Figure_5_raw_images fibers and in vivo after single injury.
Fig5F.xlsx: Quantification of Pax7-expressing cells in in Figure_5_raw_images fibers and in vivo after repeated injury.
FS3J_adult_section_Pax7.xlsx: Quantification of Pax7-expressing cells per 100 fibers (defined by Laminin staining in Fig_S3-raw-images) in WT and SMAD4 iKO muscle tissue.
FigS3H_cell_number_on_fiber_at_different_time_points.xlsx: Number of Pax7-expressing cells on wildtype and SMAD4 iKO muscle fiber at different time points after acute injury.
Fig6D.xlsx: Number of satellite cells (YFP+) in wildtype and SMAD4 iKO muscle tissue at different time points following acute injury.
Fig6C_cell_number_on_fiber_at_different_time_points.xlsx: Number of satellite cells on widltype and SMAD4 iKO muscle fibers at different time points following acute injury.
Fig5L.xlsx: Pax7+ Satellite cells per isolated muscle fiber from wild type (cntrl) and SMAD4 iKO muscle after repeated injury.
Fig5N_CTX60D_section_Pax7.xlsx: Pax7+ Satellite cells per 100 in vivo muscle fibers in wild type (cntrl) and SMAD4 iKO muscle after repeated injury.
Fig4I_quantification.xlsx: Quantification of lineage-traced transplanted muscle stem cells that have re-occupied the satellite cell niche. Pos and Neg represent Betaglycan-positive muscle stem cells and Betaglcan-negative ones.

Description of the data and file structure

I have uploaded both raw images (in TIFF or CZI format) and image quantification (Microsoft Excel sheets). Most of the images represent immuno-staining of muscle tissue based on the questions being asked in the article and after different experimental procedures. The gene expression data associated with the article has been uploaded on GEO: please see the accession number in the article.

Excel sheets are quantifications of the corresponding microscopy images. Unless indicated, numbers are actual counts. In Fig4I_quantification.xlsx, numbers indicate mouse (first number, biological replicate), particular muscle section (second number), and repeats of each number indicate multiple fields of view within that muscle section. In Fig6D.xlsx, numbers that come after 'WT' or 'KO' are arbitrarily identifying numbers for individual mice.

In the image files, specific conditions are represented by folder names, rather than file names. For example, the immono-histological images for transplanted muscle tissue that received Betaglycan-positive muscle stem cells are present in the Figure4-raw-images folder, Figure 4G sub-folder (because this is the specific figure panel in the article that has this image), and in the TGFBR3 folder. TGFBR3 is another name for Betaglycan. Also, for image file names, C1 to C5, or colors like blue, red, green, represent images from various color channels during microscopy. 'Merged' or 'composite' means the color channels are combined. The rest of the texts for particular file names are arbitrary image identifiers e.g. the file name 1_red.tif means image 1, red channel. Where letters are folder names, they are referring to Figure panels. For example, the E folder under Figure_5_raw_images folder contains images for Figure 5E in the article. iKO refers to the induced SMAD4 knock-out mutant, and WT refers to wild type.

Some of the images for the same condition are of varying brightness. This is because the pixel range was adjusted to improve the identification of nuclei. All the images were followed by adequate quantifications gotten by counting fibers and nuclei. Thus, the quantification should not be affected by brightness.

Also, among the image files, some images were reduced in dimension without affecting actual pixel content.

Sharing/Access information

Links to other publicly accessible locations of the data: Although not included here, the associated in-house-generated sequencing data can be downloaded here (raw and processed files): https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE199499
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Data was derived from the following sources: wildtype and mutant (SMAD4 iKO) mouse muscle tissue.

Code/Software

Raw microscopy images were processed using Image J as described in the article.