Sensing of extracellular L-Proline availability by the integrated stress response determines the outcome of cell competition
Data files
May 29, 2025 version files 22.94 GB
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10-P53KO-N2B27-Repeat2_S10_L003_I1_001.fastq.gz
100.14 MB
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10-P53KO-N2B27-Repeat2_S10_L003_I2_001.fastq.gz
102.45 MB
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10-P53KO-N2B27-Repeat2_S10_L003_R1_001.fastq.gz
682.35 MB
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10-P53KO-N2B27-Repeat2_S10_L003_R2_001.fastq.gz
704.10 MB
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11-Atf4KO-N2B27-Repea2_S11_L003_I1_001.fastq.gz
125.39 MB
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11-Atf4KO-N2B27-Repea2_S11_L003_I2_001.fastq.gz
124.80 MB
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11-Atf4KO-N2B27-Repea2_S11_L003_R1_001.fastq.gz
837.89 MB
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11-Atf4KO-N2B27-Repea2_S11_L003_R2_001.fastq.gz
871.57 MB
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12-DKO-N2B27-Repeat2_S12_L003_I1_001.fastq.gz
114.42 MB
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12-DKO-N2B27-Repeat2_S12_L003_I2_001.fastq.gz
120.11 MB
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12-DKO-N2B27-Repeat2_S12_L003_R1_001.fastq.gz
804.01 MB
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12-DKO-N2B27-Repeat2_S12_L003_R2_001.fastq.gz
827.57 MB
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13-E14wt-N2B27-Repeat3_S13_L003_I1_001.fastq.gz
137.42 MB
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13-E14wt-N2B27-Repeat3_S13_L003_I2_001.fastq.gz
145.01 MB
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13-E14wt-N2B27-Repeat3_S13_L003_R1_001.fastq.gz
906.31 MB
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13-E14wt-N2B27-Repeat3_S13_L003_R2_001.fastq.gz
942.10 MB
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14-P53KO-N2B27-Repeat3_S14_L003_I1_001.fastq.gz
119.27 MB
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14-P53KO-N2B27-Repeat3_S14_L003_I2_001.fastq.gz
129.03 MB
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14-P53KO-N2B27-Repeat3_S14_L003_R1_001.fastq.gz
840.53 MB
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14-P53KO-N2B27-Repeat3_S14_L003_R2_001.fastq.gz
862.26 MB
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15-Atf4KO-N2B27-Repeat3_S15_L003_I1_001.fastq.gz
123.93 MB
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15-Atf4KO-N2B27-Repeat3_S15_L003_I2_001.fastq.gz
122.76 MB
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15-Atf4KO-N2B27-Repeat3_S15_L003_R1_001.fastq.gz
850.90 MB
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15-Atf4KO-N2B27-Repeat3_S15_L003_R2_001.fastq.gz
880.63 MB
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16-DKO-N2B27-Repeat3_S16_L003_I1_001.fastq.gz
125.50 MB
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16-DKO-N2B27-Repeat3_S16_L003_I2_001.fastq.gz
131.33 MB
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16-DKO-N2B27-Repeat3_S16_L003_R1_001.fastq.gz
873.85 MB
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16-DKO-N2B27-Repeat3_S16_L003_R2_001.fastq.gz
897.69 MB
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5-E14wt-N2B27-Repeat1_S5_L003_I1_001.fastq.gz
120.51 MB
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5-E14wt-N2B27-Repeat1_S5_L003_I2_001.fastq.gz
116.33 MB
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5-E14wt-N2B27-Repeat1_S5_L003_R1_001.fastq.gz
796.43 MB
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5-E14wt-N2B27-Repeat1_S5_L003_R2_001.fastq.gz
814.29 MB
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6-P53KO-N2B27-Repeat1_S6_L003_I1_001.fastq.gz
119.05 MB
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6-P53KO-N2B27-Repeat1_S6_L003_I2_001.fastq.gz
134.49 MB
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6-P53KO-N2B27-Repeat1_S6_L003_R1_001.fastq.gz
790.63 MB
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6-P53KO-N2B27-Repeat1_S6_L003_R2_001.fastq.gz
828.08 MB
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7-Atf4KO-N2B27-Repeat1_S7_L003_I1_001.fastq.gz
113.93 MB
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7-Atf4KO-N2B27-Repeat1_S7_L003_I2_001.fastq.gz
119.52 MB
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7-Atf4KO-N2B27-Repeat1_S7_L003_R1_001.fastq.gz
757.14 MB
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7-Atf4KO-N2B27-Repeat1_S7_L003_R2_001.fastq.gz
786.35 MB
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8-DKO-N2B27-Repeat1_S8_L003_I1_001.fastq.gz
119.44 MB
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8-DKO-N2B27-Repeat1_S8_L003_I2_001.fastq.gz
124.10 MB
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8-DKO-N2B27-Repeat1_S8_L003_R1_001.fastq.gz
859.25 MB
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8-DKO-N2B27-Repeat1_S8_L003_R2_001.fastq.gz
889.98 MB
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9-E14wt-N2B27-Repeat2_S9_L003_I1_001.fastq.gz
124.22 MB
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9-E14wt-N2B27-Repeat2_S9_L003_I2_001.fastq.gz
123.93 MB
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9-E14wt-N2B27-Repeat2_S9_L003_R1_001.fastq.gz
839.06 MB
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9-E14wt-N2B27-Repeat2_S9_L003_R2_001.fastq.gz
862 MB
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README.md
3.73 KB
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RNA_SEQ_RAW_FILE_LIST_mRNA_rawfile_list_.xlsx
9.67 KB
Abstract
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
Dataset DOI: 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.