### Data from: Velasco S, Ibrahim MM, Kakumanu A, Garipler G et al. A Multi-step Transcriptional and Chromatin State Cascade Underlies Motor Neuron Programming from Embryonic Stem Cells. Cell Stem Cell 2017 Feb 2;20(2):205-217.e8. PMID: 27939218

### Generate matrix of expression

gawk '{print $1, $6}' GSM2130854_eb-nil-48hr-dox-2nd.genes.results.txt > GSM2130854_48h.R2.genes.txt
gawk '{print $1, $6}' GSM2130853_eb-nil-36hr-dox-2nd.genes.results.txt > GSM2130853_36h.R2.genes.txt
gawk '{print $1, $6}' GSM2130852_eb-nil-24hr_dox_2nd.genes.results.txt > GSM2130852_24h.R2.genes.txt
gawk '{print $1, $6}' GSM2130851_eb-nil-12hr-dox-2nd.genes.results.txt > GSM2130851_12h.R2.genes.txt
gawk '{print $1, $6}' GSM2130850_eb-nil-0hr_2nd.genes.results.txt > GSM2130850_0h.R2.genes.txt

# And the same for replicate 1
# Make a join matrix

join GSM2130845_0h.R1.genes.txt GSM2130850_0h.R2.genes.txt | join - GSM2130846_12h.R1.genes.txt | join - GSM2130851_12h.R2.genes.txt | join - GSM2130847_24h.R1.genes.txt | join - GSM2130852_24h.R2.genes.txt | join - GSM2130848_36h.R1.genes.txt | join - GSM2130853_36h.R2.genes.txt | join - GSM2130849_48h.R1.genes.txt |join - GSM2130854_48h.R2.genes.txt > genes.TPM.txt

### Select genes activated at 12h
grep -v gene_id genes.TPM.txt | sort -nk2 | gawk '{if(($2+$3)/2<1 && ($4+$5)/2>5)print $0}'
ENSMUSG00000051255.5 0.00 0.00 0.00 46.06 3.41 1.71 6.37 4.24 3.77 1.90
ENSMUSG00000066245.5 0.00 0.00 0.00 130.96 0.00 0.00 0.35 0.00 0.00 0.00
ENSMUSG00000067189.5 0.00 0.00 0.00 11.39 0.25 0.00 0.00 0.00 0.00 0.00
ENSMUSG00000068397.4 0.00 0.00 0.00 12.46 0.00 0.00 0.00 0.00 0.00 0.00
ENSMUSG00000069011.4 0.00 0.00 0.00 27.15 1.69 0.00 0.00 0.10 0.00 0.00
ENSMUSG00000076051.1 0.00 0.00 1.95 9.40 0.05 1.83 0.00 0.00 2.18 0.00
ENSMUSG00000084383.1 0.00 0.00 0.00 12.46 0.00 0.00 0.00 0.00 0.00 0.00
ENSMUSG00000090389.1 0.00 0.00 6.36 4.07 0.91 0.00 0.69 3.11 0.06 0.97
ENSMUSG00000094475.2 0.00 0.00 2.81 9.13 13.06 7.19 16.38 19.24 18.38 9.57
ENSMUSG00000094932.2 0.00 0.00 2.81 9.13 13.06 7.19 16.38 19.24 18.38 9.57
ENSMUSG00000096830.1 0.00 0.00 8.40 8.59 0.00 0.00 7.36 0.00 25.81 0.00
ENSMUSG00000100405.1 0.00 0.00 0.00 360.64 0.00 0.00 0.00 0.00 0.00 0.00
ENSMUSG00000031972.4 0.28 0.32 4.13 11.25 2.16 4.08 0.62 1.45 0.56 0.87
ENSMUSG00000032303.6 0.29 0.05 6.39 7.02 21.69 32.52 45.81 41.92 54.95 50.09
ENSMUSG00000001566.9 0.33 0.22 7.30 7.21 23.19 22.96 35.23 27.35 51.64 53.08
ENSMUSG00000068614.7 0.42 0.30 1.62 11.79 2.08 2.21 1.32 1.10 0.83 0.93
ENSMUSG00000072473.3 0.49 0.00 9.36 9.13 3.56 2.52 3.28 1.93 2.35 0.78
ENSMUSG00000027967.7 0.64 0.07 20.31 18.88 33.54 24.34 28.53 18.95 26.32 29.13
ENSMUSG00000051251.3 0.75 0.21 7.43 9.07 36.60 38.91 73.17 74.56 72.43 96.19
ENSMUSG00000051159.11 0.82 0.70 17.32 27.36 67.73 63.89 29.03 29.66 9.93 16.79
ENSMUSG00000021379.1 0.84 0.29 9.60 8.70 10.10 14.56 7.78 6.58 10.08 7.95
ENSMUSG00000032796.7 0.85 0.46 5.03 6.63 6.78 8.43 3.46 5.50 3.30 5.14
ENSMUSG00000024029.4 0.86 0.88 6.26 5.14 10.61 7.50 5.78 3.47 2.65 2.87
ENSMUSG00000025889.8 0.96 0.96 5.33 5.55 7.87 5.58 8.94 7.34 8.64 6.23
ENSMUSG00000033446.7 1.09 0.88 6.50 4.60 3.49 6.30 5.05 6.02 10.62 9.14
ENSMUSG00000036111.7 1.16 0.38 29.75 36.79 70.73 74.28 80.13 60.11 73.40 81.04
ENSMUSG00000035200.6 1.18 0.58 6.08 7.35 10.25 12.76 10.09 10.99 7.33 9.36
ENSMUSG00000065546.1 1.63 0.00 6.22 5.68 5.19 7.99 6.44 11.09 14.73 6.11

# Replicate 2 of 12h sample looks weird to me

grep -v gene_id genes.TPM.txt | sort -nk2 | gawk '{if(($2+$3)/2<1 && ($4>5))print $0}'
ENSMUSG00000064359.1 0.00 0.00 5.13 1.64 3.75 5.13 2.54 12.45 5.67 7.57
ENSMUSG00000077506.1 0.00 0.00 5.78 2.95 3.37 0.00 7.62 0.00 12.76 0.00
ENSMUSG00000081382.1 0.00 0.89 6.47 0.04 4.31 0.00 2.17 0.00 10.53 0.00
ENSMUSG00000083714.3 0.00 0.00 7.73 0.25 2.49 0.60 1.05 0.27 0.50 1.24
ENSMUSG00000090389.1 0.00 0.00 6.36 4.07 0.91 0.00 0.69 3.11 0.06 0.97
ENSMUSG00000096830.1 0.00 0.00 8.40 8.59 0.00 0.00 7.36 0.00 25.81 0.00
ENSMUSG00000098253.1 0.00 0.00 7.50 0.00 0.00 0.00 0.00 0.00 0.00 0.00
ENSMUSG00000099268.1 0.00 0.00 5.73 2.01 0.00 9.26 0.00 3.64 2.20 2.15
ENSMUSG00000032303.6 0.29 0.05 6.39 7.02 21.69 32.52 45.81 41.92 54.95 50.09
ENSMUSG00000001566.9 0.33 0.22 7.30 7.21 23.19 22.96 35.23 27.35 51.64 53.08
ENSMUSG00000072473.3 0.49 0.00 9.36 9.13 3.56 2.52 3.28 1.93 2.35 0.78
ENSMUSG00000027967.7 0.64 0.07 20.31 18.88 33.54 24.34 28.53 18.95 26.32 29.13
ENSMUSG00000051251.3 0.75 0.21 7.43 9.07 36.60 38.91 73.17 74.56 72.43 96.19
ENSMUSG00000051159.11 0.82 0.70 17.32 27.36 67.73 63.89 29.03 29.66 9.93 16.79
ENSMUSG00000021379.1 0.84 0.29 9.60 8.70 10.10 14.56 7.78 6.58 10.08 7.95
ENSMUSG00000032796.7 0.85 0.46 5.03 6.63 6.78 8.43 3.46 5.50 3.30 5.14
ENSMUSG00000024029.4 0.86 0.88 6.26 5.14 10.61 7.50 5.78 3.47 2.65 2.87
ENSMUSG00000025889.8 0.96 0.96 5.33 5.55 7.87 5.58 8.94 7.34 8.64 6.23
ENSMUSG00000033446.7 1.09 0.88 6.50 4.60 3.49 6.30 5.05 6.02 10.62 9.14
ENSMUSG00000036111.7 1.16 0.38 29.75 36.79 70.73 74.28 80.13 60.11 73.40 81.04
ENSMUSG00000035200.6 1.18 0.58 6.08 7.35 10.25 12.76 10.09 10.99 7.33 9.36
ENSMUSG00000065546.1 1.63 0.00 6.22 5.68 5.19 7.99 6.44 11.09 14.73 6.11
ENSMUSG00000098820.1 1.64 0.00 5.74 0.10 0.92 0.00 1.62 0.06 0.94 0.00


### Activated at 24h

 grep -v gene_id genes.TPM.txt | sort -nk2 | gawk '{if(($2+$3)/2<1 && ($4+$5)/2<1 && ($6+$7)/2>5)print $0}'
ENSMUSG00000065258.1 0.00 1.63 0.00 1.23 7.50 3.85 1.90 2.67 0.00 1.89
ENSMUSG00000065280.1 0.00 0.00 0.00 0.00 0.00 10.67 0.00 6.05 6.26 0.00
ENSMUSG00000022860.9 0.07 0.00 0.80 0.70 3.69 6.52 14.50 20.36 22.05 25.83
ENSMUSG00000048001.7 0.07 0.03 0.21 0.51 10.05 12.45 20.66 21.18 23.13 39.88
ENSMUSG00000027793.2 0.08 0.15 0.49 0.53 5.76 5.15 8.62 6.49 5.42 5.00
ENSMUSG00000036198.7 0.14 0.07 0.36 0.56 4.49 7.90 11.12 10.99 18.72 21.43
ENSMUSG00000023236.7 0.22 0.81 0.80 1.10 9.00 8.53 25.22 23.43 41.29 34.85
ENSMUSG00000052516.12 0.22 0.02 0.49 0.73 4.56 8.67 10.05 10.58 19.11 31.40
ENSMUSG00000039154.6 0.23 0.05 0.77 1.20 6.81 4.96 18.46 13.57 32.69 27.44
ENSMUSG00000027577.9 0.31 0.03 0.40 0.65 3.96 8.17 7.98 10.29 11.98 21.49
ENSMUSG00000025318.8 0.33 0.09 0.67 1.13 5.61 6.72 9.10 7.72 15.69 20.08
ENSMUSG00000042757.10 0.34 0.19 0.51 0.81 5.32 5.53 12.80 10.66 16.81 22.02
ENSMUSG00000043587.10 0.42 0.57 0.66 1.13 7.12 9.22 22.80 23.49 35.38 39.14
ENSMUSG00000028137.5 0.47 0.06 0.58 0.63 6.68 5.33 22.55 20.41 65.77 75.55
ENSMUSG00000003410.7 0.54 0.44 0.77 1.20 5.06 6.84 15.75 15.87 47.15 49.81
ENSMUSG00000076068.1 0.65 0.21 0.00 0.00 9.49 4.39 12.39 6.85 13.12 15.71
ENSMUSG00000022098.9 0.66 0.27 0.74 1.11 9.27 11.51 18.49 19.44 24.28 35.97
ENSMUSG00000032181.6 0.67 0.18 0.16 0.30 3.65 7.04 12.76 15.45 37.75 57.70
ENSMUSG00000027950.3 0.85 0.40 0.79 0.93 4.88 5.23 12.81 10.99 29.01 36.59