DOI: 10.5061/dryad.4b8gthtqv
title: Sensing of extracellular L-Proline availability by the integrated stress response determines the outcome of cell competition

description: To address the mechanism by which ATF4 determines the outcome of cell
 competition, we performed transcriptomic comparisons by bulk
 RNA-seq analysis of up-regulated, down-regulated and background
 genes related to the DE analysis of homogenous cultures of Atf4-/- versus
 wild-type mouse ES cells and of p53-/-; Atf4-/- versus
 p53-/- mouse ES cells at day 3 of differentiation. Differential
 cellular pathway analysis by KEGG enrichment revealed that the topmost
 downregulated pathways in both sets of cells with Atf4 mutations were
 those associated with non-essential amino acid biosynthesis, transport and
 metabolism
description: # Sensing of extracellular L-Proline availability by the integrated stress
 response determines the outcome of cell competition Dataset DOI:
 [10.5061/dryad.4b8gthtqv](10.5061/dryad.4b8gthtqv) ## Description of the
 data and file structure *Bulk RNA seq analysis of mouse ES cell
 lines-Atf4-/- and WT , p53-/- Atf4-/- and p53-/- to analyse differential
 gene expression-genes upregulated and downregulated and analyse
 differentially regulated signaling pathways and molecular functions.*
 There is a total of 12 fastq gz files and 1 Excel sheet. The 12 fastq gz
 files are 3 biological replicates for cell types-WT, p53-/- (p53KO),
 ATF4-/- (ATF4KO), and double knockout (DKO, p53-/-ATF4-/-), with 4 files
 per sample for 1 replicate/repeat. Each cell type has 3 biological
 repeats-in each repeat, there are a total of 4 fastq gz files, indicating
 4 reads for the same sample. These are labelled as:
 5-E14wt-N2B27-Repeat1_S5_L003_I1_001.fastq.gz     
 5-E14wt-N2B27-Repeat1_S5_L003_I2_001.fastq.gz     
 5-E14wt-N2B27-Repeat1_S5_L003_R1_001.fastq.gz     
 5-E14wt-N2B27-Repeat1_S5_L003_R2_001.fastq.gz for WT, repeat 1.
 6-P53KO-N2B27-Repeat1_S6_L003_I1_001.fastq.gz     
 6-P53KO-N2B27-Repeat1_S6_L003_I2_001.fastq.gz     
 6-P53KO-N2B27-Repeat1_S6_L003_R1_001.fastq.gz     
 6-P53KO-N2B27-Repeat1_S6_L003_R2_001.fastq.gz for p53-/- repeat 1.
  7-Atf4KO-N2B27-Repeat1_S7_L003_I1_001.fastq.gz   
 7-Atf4KO-N2B27-Repeat1_S7_L003_I2_001.fastq.gz   
 7-Atf4KO-N2B27-Repeat1_S7_L003_R1_001.fastq.gz   
 7-Atf4KO-N2B27-Repeat1_S7_L003_R2_001.fastq.gz for ATF4-/- repeat 1
 8-DKO-N2B27-Repeat1_S8_L003_I1_001.fastq.gz      
 8-DKO-N2B27-Repeat1_S8_L003_I2_001.fastq.gz      
 8-DKO-N2B27-Repeat1_S8_L003_R1_001.fastq.gz      
 8-DKO-N2B27-Repeat1_S8_L003_R2_001.fastq.gz for p53-/- ATF4-/-, repeat 1
 9-E14wt-N2B27-Repeat2_S9_L003_I1_001.fastq.gz    
 9-E14wt-N2B27-Repeat2_S9_L003_I2_001.fastq.gz    
 9-E14wt-N2B27-Repeat2_S9_L003_R1_001.fastq.gz    
 9-E14wt-N2B27-Repeat2_S9_L003_R2_001.fastq.gz for WT, repeat 2  
 10-P53KO-N2B27-Repeat2_S10_L003_I1_001.fastq.gz  
 10-P53KO-N2B27-Repeat2_S10_L003_I2_001.fastq.gz  
 10-P53KO-N2B27-Repeat2_S10_L003_R1_001.fastq.gz  
 10-P53KO-N2B27-Repeat2_S10_L003_R2_001.fastq.gz for p53-/- repeat 2.
 11-Atf4KO-N2B27-Repea2_S11_L003_I1_001.fastq.gz 
 11-Atf4KO-N2B27-Repea2_S11_L003_I2_001.fastq.gz 
 11-Atf4KO-N2B27-Repea2_S11_L003_R1_001.fastq.gz 
 11-Atf4KO-N2B27-Repea2_S11_L003_R2_001.fastq.gz for ATF4-/- repeat 2
 12-DKO-N2B27-Repeat2_S12_L003_I1_001.fastq.gz    
 12-DKO-N2B27-Repeat2_S12_L003_I2_001.fastq.gz    
 12-DKO-N2B27-Repeat2_S12_L003_R1_001.fastq.gz    
 12-DKO-N2B27-Repeat2_S12_L003_R2_001.fastq.gz for p53-/- ATF4-/-, repeat
 2. 13-E14wt-N2B27-Repeat3_S13_L003_I1_001.fastq.gz  
 13-E14wt-N2B27-Repeat3_S13_L003_I2_001.fastq.gz  
 13-E14wt-N2B27-Repeat3_S13_L003_R1_001.fastq.gz  
 13-E14wt-N2B27-Repeat3_S13_L003_R2_001.fastq.gz for WT, repeat 3 
 14-P53KO-N2B27-Repeat3_S14_L003_I1_001.fastq.gz  
 14-P53KO-N2B27-Repeat3_S14_L003_I2_001.fastq.gz
 14-P53KO-N2B27-Repeat3_S14_L003_R1_001.fastq.gz
 14-P53KO-N2B27-Repeat3_S14_L003_R2_001.fastq.gz for p53-/- repeat 3
 15-Atf4KO-N2B27-Repeat3_S15_L003_I1_001.fastq.gz
 15-Atf4KO-N2B27-Repeat3_S15_L003_I2_001.fastq.gz
 15-Atf4KO-N2B27-Repeat3_S15_L003_R1_001.fastq.gz
 15-Atf4KO-N2B27-Repeat3_S15_L003_R2_001.fastq.gz for ATF4-/- repeat 3
 16-DKO-N2B27-Repeat3_S16_L003_I1_001.fastq.gz
 16-DKO-N2B27-Repeat3_S16_L003_I2_001.fastq.gz
 16-DKO-N2B27-Repeat3_S16_L003_R1_001.fastq.gz
 16-DKO-N2B27-Repeat3_S16_L003_R2_001.fastq.gz for p53-/- ATF4-/-, repeat
 3. The Excel sheet- TITLED- "RNA_SEQ_RAW_FILE_LIST_mRNA_rawfile_list
 " has a list of all 12 samples' gz files.