11 different TF deletion strains
a digital expression matrix was provided in the supporting doc.
from scRNA counts per gene to gene regulatory network, the author used "inferelator", a regression based method.
A gold-standard prior TF-network was cited from Tchourine, 2018. which include 1403 signed (-1, 0, 1) interactions in a 998 genes by 98 transcription factor regulatory matrix.
Another unsigned gene network cited Teixeira 2018 that include 11486 interactions in a 3912 genes by 152 TFs.
A multi-task fitting was used to infer a gene network to 11 conditions.
The cellranger pipeline is available from 10x Genomics under the MIT license (https://github.com/
10XGenomics/cellranger). The fastqToMat0 pipeline is available from GitHub (https://github.com/
flatironinstitute/fastqToMat0; Jackson, 2020; copy archived at https://github.com/elifesciences-pub-
lications/fastqToMat0) and is released under the MIT license. Genome sequence and annotations
are included as Source code 4.
# Included in this archive are the following data files:
# data/
# 103118_SS_Data.tsv.gz (TSV count matrix of single-cell yeast reads [cells x genes])
# 110518_SS_NEG_Data (TSV count matrix of simulated single-cell reads [cells x genes])
# TRIZOL_BULK.tsv (TSV count matrix of data prepared with TRIZOL [samples x genes])
# yeast_gene_names.tsv (TSV with Systematic Names and Common Names for yeast genes)
# STable5.tsv (TSV copy of Supplemental Table 5 with cross-validation results)
# STable6.tsv (TSV copy of Supplemental Table 6 with genes grouped into categories)
# go_slim_mapping.tab (GO Slim Terms: https://downloads.yeastgenome.org/curation/literature/go_slim_mapping.tab)
# go_slim_labels.tsv (TSV with shorter figure names for GO slim terms)
# GASCH_2017_COUNTS.tsv (TSV from GSE102475; Gasch 2017 BY4741 single-cell TPM data in mid-log YPD [cells x genes])
# LEWIS_ALL.tsv (TSV from GSE135430; Scholes 2019 BY4741 bulk TPM data in mid-log YPD[samples x genes])
# LARS_2019_COUNTS.tsv (TSV from GSE122392; Nadal-Ribelles 2019 BY4741 single-cell count data in mid-log YPD [cells x genes])
# inferelator/
# jackson_2019_figureXX.py (Python script to run the network inference with the inferelator v0.3.0 for the associated figure)
# network/
# signed_network.tsv (TSV signed [-1, 0, 1] network of regulatory relationships [genes x TFs])
# COND_signed_network.tsv (TSV signed [-1, 0, 1] network of regulatory relationships [genes x TFs] for each of 11 conditions)
# priors/
# Tchourine_gold_standard.tsv.gz (TSV with gold standard from Tchourine et al 2018)
# ATAC-motif_priors.tsv.gz (TSV with atac-motif priors from Castro et al 2019)
# YEASTRACT_priors_20181118.tsv.gz (TSV with YEASTRACT priors downloaded from YEASTRACT 11/18/2018)
# YEASTRACT_20190713_BOTH.tsv (TSV with YEASTRACT priors downloaded from YEASTRACT 07/13/2019)
# YEASTRACT_20190713_DNABINDING.tsv (TSV with YEASTRACT DNA-binding interaction data downloaded from YEASTRACT 07/13/2019)
# YEASTRACT_20190713_EXPRESSION.tsv (TSV with YEASTRACT expression change interaction data downloaded from YEASTRACT 07/13/2019)
# BUSSEMAKER_priors_2008.tsv.gz (TSV with priors from Ward & Bussemaker 2008)
Source code 1
A ‘tar.gz’ archive containing R scripts used to generate Figures 2–7 and accompanying supplementary figures with a README detailing the necessary R environment to run them locally.
It also contains a data folder with the raw count matrix as a TSV file (103118_SS_Data.tsv.gz), the simulated negative data count matrix as a TSV file (110518_SS_NEG_Data.tsv.gz), a gene name metadata TSV file (yeast_gene_names.tsv), supplemental tables 5 (STable5.tsv) and 6 (STable6.tsv) as TSV files, and the yeast gene ontology slim mapping as a TAB file (go_slim_mapping.tab). Source code 1 also contains a priors folder with the Gold Standard, the three sets of priors data tested in this work, and the YEASTRACT comparison data, all as TSV files. Source code 1 also contains a network folder with the network learned in this paper (signed_network.tsv) as a TSV file, and the networks for each experimental condition (COND_signed_network.tsv) as 11 separate TSV files. Source code 1 also contains an inferelator folder with the python scripts used to generate the networks for Figures 5, 6, 7.
- https://cdn.elifesciences.org/articles/51254/elife-51254-code1-v3.tar.gz
Source code 2
The raw count matrix as a gzipped TSV file.
This file contains 38,225 observations (cells). Doublets and low-count cells have already been removed; gene expression values are unmodified transcript counts after deartifacting using UMIs (these values are directly produced by the cellranger count pipeline)
- https://cdn.elifesciences.org/articles/51254/elife-51254-code2-v3.tsv.gz
Source code 3
The network learned in this paper as a TSV file.
- https://cdn.elifesciences.org/articles/51254/elife-51254-code3-v3.tsv
Source code 4
A ‘.tar.gz’ archive containing the sequences used for mapping reads.
It also contains a FASTA file containing the genotype-specific barcodes (bcdel_1_barcodes.fasta), a FASTA file containing the yeast S288C genome modified with markers (Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.Marker.fa), and a GTF file containing the yeast gene annotations modified to include untranslated regions at the 5’ and 3’ end, and with markers (Saccharomyces_cerevisiae.R64-1-1.Marker.UTR.notRNA.gtf).
- https://cdn.elifesciences.org/articles/51254/elife-51254-code4-v3.tar.gz
Source code 5
A zipped HTML document containing the raw R output figures for Figures 2–7 and accompanying supplementary Figures.
The R markdown file to create this document is contained in Source code 1.
- https://cdn.elifesciences.org/articles/51254/elife-51254-code5-v3.zip
Supplementary file 1
An excel file containing Supplemental Tables 1-6.
Supplemental Table 1 contains all primer sequences used in this work. Supplemental Table 2 contains all Saccharomyces cerevisiae strains used in this work. Supplemental Table 3 contains all plasmids used in this work. Supplemental Table 4 contains all media formulations used in this work. Supplemental Table 5 contains the source data for modeling performance (as AUPR) that is reported graphically in Figure 5. Supplemental Table 6 contains the gene categorizations (cell cycle stage, RP, RiBi, etc) used in Figure 3.
- https://cdn.elifesciences.org/articles/51254/elife-51254-supp1-v3.xlsx
Transparent reporting form
- https://cdn.elifesciences.org/articles/51254/elife-51254-transrepform-v3.pdf
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