This folder contains all the data, raw, intermediate, and processed from the manucript "Simultaneous CRISPR screening and spatial transcriptomics reveals intracellular, intercellular, and functional transcriptional circuits"

astrocytes/raw/sample1and2/MERFISH
astrocytes/raw/sample1and2/perturbations
astrocytes/raw/sample3and4/MERFISH
astrocytes/raw/sample5/MERFISH
astrocytes/raw/sample5/perturbations
astrocytes/masks/
astrocytes/processed/sample1and2/MERFISH
astrocytes/processed/sample3and4/MERFISH
astrocytes/processed/sample5/MERFISH
astrocytes/processed/finaltables
astrocytes/extras/calcium/
extras/THP1/raw/sample1/MERFISH
extras/THP1/raw/sample1/perturbations
extras/THP1/raw/sample2/MERFISH
extras/THP1/raw/sample2/perturbations
extras/THP1/processed/sample1/MERFISH
extras/THP1/processed/sample2/MERFISH
extras/THP1/processed/finaltables
extras/tumors/raw/sample1/MERFISH/
extras/tumors/raw/sample1/perturbations
extras/tumors/processed/sample1/MERFISH/
extras/tumors/processed/finaltables

Regarding the astrocyte data, "sample" refers to one well containing astrocytes, which was used to generate one time lapse video and one transcriptomic dataset. samples 1 and 2 are wells that were together on one coverslip, therefore their transcriptomics data are provided together. Similarly, samples 3 and 4 were together on one coverslip. These "samples" names match the sample names used in the folder that contains the segmentation masks, and in the folder "calcium", inside "extra", which contains the images from the time lapses videos. The THP1 and tumor datasets are provided in the folder extras. The THP1 raw data is provided as two different samples (each are a different coverslip, and each of them contains 2 wells that are just replicates and are grouped together). The data was processed together, and output tables are available in the processed folder. 
The MERFISH data for the astrocytes and the tumor data is formated as MERSCOPE data, the spreadsheet (codebook, dataorganization) necessary for data processing are available in the processed "folders". The MERFISH data for the THP1s has a different format because it was generated on the prototype of the MERSCOPE. The tables necessary for processing are also provided in the processed folders.

A full protocol describing the technology introduced in this work is available at protocols.io: https://dx.doi.org/10.17504/protocols.io.6qpvr356bvmk/v1 Experimental details are provided in the STARS methods section of the manuscript. For the perturbations, all imaging was performed on a prototype version of the MERSCOPE. For the transcriptome part, the THP1 data was imaged on the same prototype microscope, while the astrocytes and the tumor were imaged on a MERSCOPE.

Computational analysis was performed in two parts: the decoding of the MERFISH signal was performed using the google cloud compute platform, using MERlin: https://github.com/lbinan/gcp_merlin ; the rest of the analysis was performed on a local cluster, using custom scripts that are available in GitHub.