Cell Systems

Raw data and analysis codes for paper entitled "Linear Regression Links Transcriptomic Data and Cellular Raman Spectra".

We hypothesized that nerve growth factor (NGF)-mediated Erk1/2 phosphorylation is differently modulated in subpopulations of primary sensory neurons when neurons are cultured on poly-D-lysine (PDL) versus collagen type I (Col I). For this, dissociated sensory neurons from dorsal root ganglia of male Sprague Dawley rats were cultured overnight on PDL or Col I and were stimulated acutely with NGF (kinetic: 0, 1, 5, 15, 30, 60, 120 min and 20 ng/ml; dose response: 1h and 0, 0.16, 0.8, 4, 20, 100, 500 ng/ml). NGF-induced signaling activity was monitored by detecting phosphorylated Erk1/2 via immunocytochemistry with phospho-specific antibody labelling (NGF kinetic (file: KM14_KM28KM31KM34_NGFkinetic_pErk_ResultsFinal_Cells) and NGF dose response (file: KM14_KM60KM62KM67KM68_NGFdoseresponse_pErk_ResultsFinal_Cells)). Additionally, co-labelling with antibodies against TrkA (receptor of NGF, file: KM14_KM100KM102KM104KM106_NGFdoseresponse_TrkApERK_ResultsFinal_Cells) and Erk1/2 (file: KM14_KM101KM103KM105KM107_NGFdoseresponse_ERKpERK_ResultsFinal_Cells) should determine differences in these pathway components between PDL/NGF and Col I/NGF treated sensory neurons. Cultures were fully digitalized by the Cellomics ArrayScan XTi HCS microscope and analyzed on a single-cell level by automated image analysis algorithms and R-script processing. NGF kinetic and dose response data show a significant amplitude increase of Erk1/2 phosphorylation in Col I treated cultures. pErk/TrkA and pErk/Erk data present an increase in TrkA and Erk1/2 expression in Col I treated cultures. This experimental single-cell data was used to demonstrate the capacity of our novel hierarchical, data-driven approach to modeling single-cell populations. File description (header): PlateID: Plate IDs corresponding to labbook entries of 3-4 replicate experiments Well: corresponding wells of 96-well plate Stain: Staining of wells with corresponding antibody combinations for spill over compensation of fluorescent channels (Ch1, Ch1Ch2, Ch1Ch3, Ch1Ch2Ch3) Cond: treatment condition (PDL: poly-D-lysine; Col I: collagen type I, SpillOver: for data compensation) Comp: applied compound (Ctrl: solvent, NGF: nerve growth factor, Fsk: forskolin (positive control)) Conc: used concentration (ng/ml) or if not applicable tested wells Time: stimulation time (min) Area: Cell size in µm2 Ch1-Ch4: fluorescent intensities of indicated antibody stainings (ch-UCHL1: chicken polyclonal antibody against UCHL1; rb-pErk: rabbit monoclonal antibody against phospho-Erk1/2; mm-UCHL1: mouse monoclonal antibody against UCHL1; go-TrkA: goat polyclonal antibody against TrkA; mo-Erk1/2: mouse monoclonal antibody against ERK1/2)

Raw mass cytometry and imaging mass cytometry data used to develop the compensation tool available within the R package CATALYST

Raw data for Staller et al. 2018 A high-throughput mutational scan of an acidic transcriptional activation domain Max V. Staller1, 2, Alex S. Holehouse3,4, Devjanee Swain-Lenz1,2,5, Rahul K. Das3,4,6, Rohit V. Pappu3,4, and Barak A. Cohen1, 2, * 1Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, Saint Louis, MO, 63110 2Department of Genetics, Washington University in St. Louis School of Medicine, Saint Louis, MO, 63110 3Department of Biomedical Engineering, Washington University in St. Louis, Saint Louis, MO, 63130 4Center for Biological Systems Engineering, Washington University in St. Louis, Saint Louis, MO, 63130 5Present address: Department of Biology, Duke University, Durham, NC, 27708 6Present address: GNS Healthcare Inc., Cambridge, MA, 02139 * Corresponding Author and Lead contact: cohen@wustl.edu Files include: raw sequencing reads for replicate 1 (Sort 11) raw sequencing reads for replicate 2 (Sort 12 ) raw sequencing reads for replicate 1 of amino acid starvation condition (Sort 14) for calculating induction raw sequencing reads for mCherry only sorting (sort 15A) File of designed mutants (DNA sequence) (DNA_Seqs_GCN4_Array.txt). raw sequencing reads for paired end sequencing to look for mutations in the library (Sort11AD-BC R1 and R2) Key to barcodes: Sort_Bin 5’ inline barcode 3’ adaptor barcode S11_1 GCTCGAT IND71 S11_2 TAGACTAT IND71 S11_3 CGCTACCCT IND71 S11_4 ATAGTGGACA IND71 S11_5 GCTCGAT IND72 S11_6 TAGACTAT IND72 S11_7 CGCTACCCT IND72 S11_8 ATAGTGGACA IND72 S12_1 GCTCGAT IND69 S12_2 TAGACTAT IND69 S12_3 CGCTACCCT IND69 S12_4 ATAGTGGACA IND69 S12_5 GCTCGAT IND70 S12_6 TAGACTAT IND70 S12_7 CGCTACCCT IND70 S12_8 ATAGTGGACA IND70 S14_1 GCTCGAT IND69 S14_2 TAGACTAT IND69 S14_3 CGCTACCCT IND69 S14_4 ATAGTGGACA IND69 S14_5 GCTCGAT IND70 S14_6 TAGACTAT IND70 S14_7 CGCTACCCT IND70 S14_8 ATAGTGGACA IND70 S15_1 GCTCGAT IND69 S15_2 TAGACTAT IND69 S15_3 CGCTACCCT IND69 S15_4 ATAGTGGACA IND69 S15_5 GCTCGAT IND70 S15_6 TAGACTAT IND70 S15_7 CGCTACCCT IND70 S15_8 ATAGTGGACA IND70

This dataset contains the raw data images, mask files for single cell segmentation, meta data as well as single cell data from the publication "Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry".

Data_S1 is a Matlab file containing the growth curves of six liquid-culture experiments used in Figures 1 and 2, obtained with an automated robotic system at 30ºC. The 'Experiment' field includes a reference to the panels in the main text where the data is used, and the 'Info' field specifies how tetracycline was added to the cultures. The 'Data' field contains optical density (OD) and fluorescence (when applicable) measurements for each strain used in the experiment, together with vectors specifying the gradients of IPTG and tetracycline used (when applicable), the time of the measurements, indication of each type of measurement performed and times of IPTG induction (in Fig. 1F). A detailed description of the methods and strains used is given in the STAR Methods section. Data_S2 contains the image files obtained with the microfluidic device, where cells carrying the native tet resistance mechanism were exposed to a step increase of 70μg/ml tetracycline at time zero. Images were taken every 10 minutes at 10 different positions in 3 different fluorescence channels. CFP was expressed constitutively and used for image segmentation. GFP was expressed from the same promoter as TetR and mCherry was expressed from the same promoter as TetA. The file name indicates the time, position and fluorescence channel. A detailed description of the experiment and the strain used is given in the STAR Methods section.

Sample data for juicebox.js

Matlab scripts for the Refractory Model, Dunham et al.

Single-cell gene expression data generated using 96x96 fluidigm dynamic arrays. Experimental details including steps to reproduce data are included in the associated manuscript. Briefly, mouse embryonic stem cells kept in 2i+LIF conditions for four passages differentiated towards the neuronal lineage in N2B27 medium as described in the literature (Ying et al. 2003 - DOI: 10.1038/nbt780). At 0h, 24h, 48h, 72h, 96h, 120h and 168h individual cells were sorted by FACS based on light-scatter properties and deposited into 96-well plates containing lysis buffer and RT reagents before processing for qPCR using the Biomark HD.

Amino acids in CDM35 medium conditioned with five different S. cerevisiae strains. Only amino acids not present in CDM35 were quantified. Concentrations are given in nM, corresponding OD600 values are also provided.