Cell Reports

Raw data and original images: "The interaction of the tumor suppressor FAM46C with p62 and FNDC3 proteins integrates protein and secretory homeostasis" Fucci et al. Cell Reports 2020. Descriptions of data and methods are included in the Cell Reports manuscript. RAW files generating Datasets 1-3 in the manuscript are present in the Proteomics folder. Raw data/original images are organized according to the associated figure panel.

Modeled data generated by a Bayesian dose-response framework predicting sequentially effective drug combinations from an oncological drug matrix screen, comprising 10,000 drug combinations in melanoma and pancreatic cancer cell lines.

To reveal distinct transcriptomes associated with various spermatogenic cells in both mouse and human testes, including spermatogonial stem cells (SSCs) and all of their subsequent progeny, we used the 10x Genomics Chromium (a commercialized Drop-Seq variant) to perform single-cell RNA-seq on various cell populations. Raw data and analyzed data (gene expression matrices) are deposited into the NIH GEO database. Here we include queryable, annotated and interactive files that can be used to compare single-cell transcriptomes. Spermatogonia from immature (P6) and adult Id4-Egfp transgenic mice were used. The GFP-bright and dim phenotypes exhibit distinct fates when assayed by transplantation, with ID4-EGFPbright cells highly enriched for SSCs, and ID4-EGFPdim cells enriched for progenitors. Corresponding human spermatogonia were enriched from human testicular tissue by multi-parameter FACS. For both human and mouse, StaPut gravity sedimentation enriched for meiotic spermatocytes and post-meiotic spermatids and we profiled unselected steady-state spermatogenic cells. The data from these experiments are stored in Loupe Cell Browser files (.cloupe) which are generated during analysis of 10x Genomics Single-cell data and can be opened and queried with the Loupe Cell Browser (10X Genomics). This software can be downloaded for free from https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest. It is important to note that the companion manuscript for these data used additional analyses that are not represented in these files. The following datasets are available: 1. Unselected or sorted P6 ID4-EGFP+ spermatogonia (sorted separately as EGFP-bright or EGFP-dim) were used for this study. Data are from 13094 cells and can be found in the following file: P6 Mouse Spermatogonia.cloupe (aggregate of three datasets, P6 ID4-EGFP bright/dim/unselected) 2. Unselected or sorted Adult ID4-EGFP+ spermatogonia (sorted separately as EGFP-bright or EGFP-dim), three replicate preparations of steady-state unselected spermatogenic cells, and StaPut-enriched adult spermatocytes and spermatids were used for this study. Data are from 17491 cells and can be found in the following files: Adult Mouse Sorted Spermatogonia.cloupe (Aggregated Ad Spg- ID4-EGFP bright/dim/CD9bright) Mouse Unselected Spermatogenic cells.cloupe (3 replicates of steady-state spermatogenic cells) Mouse StaPut Spermatocytes.cloupe Mouse StaPut Spermatids.cloupe 3. Sorted adult Human spermatogonia, three replicates of steady-state unselected spermatogenic cells, and StaPut-enriched adult spermatocytes and spermatids were used. Data are from 32727 cells and can be found in the following files: Human Sorted Spermatogonia.cloupe (3 replicates) Human Unselected Spermatogenic Cells.cloupe (3 replicates of steady-state spermatogenic cells) Human StaPut Spermatocytes.cloupe (2 replicates) Human StaPut Spermatids.cloupe (2 replicates)

Raw and analyzed data, and custom-written codes of Yamada et al., Cell Reports (2018) "Light control of the Tet-gene expression system in mammalian cells".

Raw data for Westerns, autoradiogram and imaging

Pull-down experiments using as bait Nup153-NTD[aa1-245](negative control) or [aa1-339] and whole cell extracts from WT (HM1) or Nup133-/- (KO, #14) mESCs. Inputs (1x equivalent) and eluates (64x equivalent, dataset (i) or 48x equivalent, dataset (ii)) were analyzed by western blot. These western blots revealed a similar enrichment of Tpr and Y-complex proteins (Nup107,Nup96, Nup85) in Nup153-NTD [aa 1-339]-purified extracts from either WT or Nup133-/- mESCs. Anti-Nup98 and GAPDH were used as negative controls. The zip-file includes 2 folders correspond to datasets (i): Souquet et al Figure 4D (i, 64x eluates) and (ii): Souquet et al Figure 4D (ii, 48x eluates), respectively. In the dataset (ii), 3 independently processed eluates were analyzed. Each folder encompasses a general montage, in which the areas used for Figure 4C are indicated in red, as well as 5 sub-folders corresponding to the original 16-bit images (each include the ECL signal and the image of the membrane to visualize the molecular markers). For each pull-down experiment, the same samples were loaded on both nitrocellulose (that was stained with Ponceau) and PVDF membranes. - The top of the nitrocellulose membrane was first probed with Nup107, cut, and reprobed with anti-Nup133 His-Nup153 pull-down (nitro I or ii) Nup107 His-Nup153 pull-down (nitro I or ii) Nup133 (rehybr after Nup107) - The bottom of the nitrocellulose membrane was probed with anti-GAPDH antibody His-Nup153 pull-down (nitro i) GAPDH - The PVDF membrane was first cut and probed with Tpr, Nup96 and Nup85 His-Nup153 pull-down (PVDF i)Tpr-Nup96-Nup85 - The part of the PVDF membrane probed wiuth Nup98 was then reprobed with anti Nup98 His-Nup153 pull-down (PVDF i)_Nup98 (rehyb from Nup96)

Original data of images and Western blot from the paper: Mind bomb regulates cell death during TNF signaling by suppressing RIPK1’s cytotoxic potential

Original data of immunofluorescence, chemiluminescence, and autoradiography

All metabolomics and lipodomic data

Liver cells stained for protein expression by immunostaining in Figure 1G, 2H, 5B and 6D.