Carlos-Francisco Méndez-Cruz / automatic-extraction-growth-conditions

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Estefani Gaytan Nunez
b4a0ecbb 1 parent 6ae98d6d

almacenado y renombrado en Nuevo-Dropbox

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Showing 4 changed files with 1 additions and 241 deletions
...@@ -299,7 +299,7 @@ if __name__ == "__main__": ...@@ -299,7 +299,7 @@ if __name__ == "__main__":
299 299
300 # Original: labels = list(crf.classes_) 300 # Original: labels = list(crf.classes_)
301 # Original: labels.remove('O') 301 # Original: labels.remove('O')
302 - labels = list(['Air', 'Gtype', 'Gversion', 'Med', 'Phase', 'Sample', 'Serie', 'Strain', 'Supp', 'Technique', 'Temp', 'OD', 'Anti', 'Agit', 'Vess']) 302 + labels = list(['Air', 'Gtype', 'Gversion', 'Med', 'Phase', 'Supp', 'Technique', 'Temp', 'OD', 'Anti', 'Agit', 'Vess'])
303 303
304 # use the same metric for evaluation 304 # use the same metric for evaluation
305 f1_scorer = make_scorer(metrics.flat_f1_score, 305 f1_scorer = make_scorer(metrics.flat_f1_score,
......
1 -!Sample_characteristics_ch1 !Sample_characteristics_ch2 !Sample_data_processing !Sample_extract_protocol_ch1 !Sample_growth_protocol_ch1 !Sample_growth_protocol_ch2 !Sample_library_strategy !Sample_organism_ch1 !Sample_organism_ch2 !Sample_source_name_ch1 !Sample_source_name_ch2 !Sample_title !Sample_treatment_protocol_ch1
2 -Med Substrain Technique Phase Med Med Technique Substrain Orgn Supp Name Name Supp
3 -Orgn Med Gversion Vess Agit Gversion Strain Gtype Phase
4 -Strain Gtype Temp Temp Orgn Name OD
5 -Supp Supp Supp Air Name Air Temp
6 -Air Air OD Med
7 -Substrain Air
8 -Anti Phase
9 -Phase Gtype
10 -Gtype Agit
1 -Agit Air Anti Gtype Gversion Med Name OD Orgn Phase Strain Substrain Supp Technique Temp Vess
2 -gyratory water bath shaking at 240 rpm aerobically (25% O2, 70% N2 and 5% CO2) 9E10 Myc tag fur-8myc NC_000913.2 M63 minimal glucose Fur IP ChIP-Seq Anaerobic A OD600 of ~0.3-0.35 Escherichia coli str. K-12 substr. MG1655 exponential K-12 MG1655 20 min RNA-Seq 30 °C (see control sample) flask
3 - anerobically (95% N2, 5% CO2) Affinity Purified FNR antibody delta_cra U00096.2 M63 σ32 30°C rep1 O.D.600nm 0.3 K-12 MG1655 mid-log phase MG1655star 100ug/L adenine ChIP-Seq 37 °C
4 - Aerobic anti-Fur polyclonal antibody ∆fnr ASM584v2 LB Fur IP ChIP-Seq Anaerobic C OD600 of 2.0 Escherichia coli mid-log Fe and rifampicin ChIP-exo 30 degrees C
5 - aerobically affinity purified anti-Fur antibody dFNR (PK4854) NC_000913 M9 minimal complete media Fur IP ChIP-Seq Anaerobic B OD600 ≈ 0.5 Escherichia coli K-12 mid-log phase Fe 30 °C
6 - anaerobic SeqA oxyR-8myc NC_000913 glucose (2 g/L) minimal M9 medium LB 0.4 B2 TEX pos L1 HS2 OD600 of 0.35 MG1655 mid-log pahse Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final) 37°C
7 - anaerobically (95% N2 and 5% CO2) anti-RpoS WT ChIP-Seq M9 minimal media LB 0.4 B2 TEX pos L1 HS1 OD600 of 0.3 Escherichia coli str. K-12 substr. MG1655star stationary acetate 43 °C
8 - anaerobically Pre-cleared IHF polyclonal antibody wild type LB media Wild type control (10 min) OD600 of about 0.3 150 mg/mL 43 °C (see heat sample)
9 - aerobically (70% N2, 25% O2, and 5% CO2) anti-myc Wild-Type L broth LB 0.4 B1 TEX pos L1 GA OD600 of ~0.4 16 µM IPTG and 300 µL Cm20 37°C
10 - Anaerobic anti-RpoB Wildtype M9 medium σ32 30°C rep2 OD600 of about 0.15 DPD
11 - Pre-cleared FNR antibody lacking the transcription factor Fur and the small RNA RyhB MOPS ChIP-exo GadX pH5.5 2 2g/L glutamine
12 - σ32 gadX-8myc glucose (2 g/L) minimal W2 medium ChIP-exo GadX pH5.5 1 absence of 1 g/L arginine
13 - RNA polymerase subunit β lacking the transcription factor Fur M9 minimal medium NsrR_Flagtag_rep3 2 g/L glucose
14 - none crp Knock-out strain MOPS minimal glucose media NsrR_Flagtag_rep2 4 µM IPTG
15 - RNA Polymerase ß monoclonal antibody TrpR-8myc NsrR_Flagtag_rep1 16 µM IPTG
16 - anti-FLAG mAb PhtpG::lacZ delta lacX74/ptrc99A (control vector) RpoB WT 2 8 µM IPTG and 300 µL Cm20
17 - Pre-cleared H-NS polyclonal antibody cra-8myc-tagged RpoB WT 1 1g/L arginine
18 - anti-rpoB dFNR Ecoli_wild-type_rep2_anaerobic 0.2% fructose
19 - gadW-8myc HNS - Aerobic A 0.3 M of NaCl
20 - wildtype HNS - Aerobic B 0.2% acetate
21 - PK4854 ∆fnr - Anaeroibc 0.2%
22 - {delta}lacZ, {delta}tonB, {delta}feoA, {delta}zupT K12 TrpR_glucose DPD and rifampicin
23 - gadE-8myc WT_ChIPSeq_2 1 µM FeSO4
24 - Combined input ChIP-exo GadE pH5.5 2 20 mg/L tryptophan
25 - delta-gadE ChIP-exo GadE pH5.5 1 250 uM of paraquat
26 - ompR-8myc WT_ChIPSeq_1 0.1mM of FeCl2
27 - lacking the small RNA RyhB WT PQ 2 Adenine
28 - Flag-tag ChIP-exo GadW pH5.5 1 rifampicin dissolved in methanol
29 - {delta}tonB, {delta}feoA, {delta}zupT K12 OmpR NaCl 2 nitrate
30 - PhtpG::lacZ delta lacX74/pTG2 (vector carrying inducible Ptrc::rpoH) OmpR NaCl 1 0.2% glucose
31 - delta-gadX ChIP-exo GadW pH5.5 2 fructose
32 - delta-gadW Ptac::fnr - A - 8 µM IPTG 10 µM FeSO4
33 - PurR-8myc SeqA old deltaSeqA 8 µM IPTG
34 - delta-oxyR ΔgadW pH5.5 1 0.2mM of DPD
35 - soxR-8myc ΔoxyR PQ 1 2 hours
36 - ΔseqA ΔoxyR PQ 2 30 min
37 - PK8263 ΔgadW pH5.5 2 4 µM IPTG and 300 µL Cm20
38 - delta-soxS ∆ryhB Aerobic presence or absence of 1 g/L arginine
39 - delta-soxR σ32 ChIP DNA, heat 1mM IPTG
40 - ∆hns/∆stpA Δfur with Fe 2 (RNA-seq) glucose
41 - soxS-8myc RpoH induced (20 min) 2h
42 - Wild-type SoxR PQ 1 10 mM leucine
43 - Δfur SoxR PQ 2
44 - Lrp-8myc LB 2.0 B2 TEX neg L1 HS1
45 - ArgR-8myc PurR_glucose_2
46 - NsrR PurR_glucose_1
47 - cra Knock-out strain LB 2.0 B2 TEX neg L1 HS2
48 - ompR deletion mutant SeqA new rep2
49 - WT with Fe 2 (RNA-seq)
50 - RpoH induced (2.5 min)
51 - Δcra acetate 1
52 - Δcra acetate 2
53 - Nac_ChIPSeq
54 - EC18n185 RpoH 10 min Time course 3
55 - σ32 43°C rep2
56 - RpoB with Fe 1 (ChIP-exo)
57 - CsiR_RNASeq
58 - ΔsoxR PQ 1
59 - EC18n169 RpoH 5 min Time course 2
60 - CsiR_ChIPSeq
61 - HNS - Anaerobic A
62 - Fur IP ChIP-Seq Aerobic A
63 - Fur IP ChIP-Seq Aerobic B
64 - HNS - Anaerobic B
65 - σ32 43°C rep1
66 - LB 2.0 B1 TEX pos L2 HS2
67 - OxyR PQ 2
68 - Wild type control (0 min)
69 - WT acetate 1
70 - WT acetate 2
71 - M63 0.4 B2 TEX pos L1 HS1
72 - M63 0.4 B2 TEX pos L1 HS2
73 - SeqA new rep1
74 - SeqA old rep2
75 - IHF - Anaerobic B
76 - IHF - Anaerobic A
77 - RNAP old rep2
78 - RpoH induced (0 min)
79 - EC18n180 RpoH 10 min Time course 1
80 - EC18n122 RpoH 10 min Time course 4
81 - LB 2.0 B2 TEX pos L1 HS1
82 - Crosslink
83 - LB 2.0 B2 TEX pos L1 HS2
84 - Cra glucose 1
85 - Cra glucose 2
86 - Cra fructose 1
87 - Cra fructose 2
88 - Wild-type Aerobic A
89 - Wild-type Aerobic B
90 - RpoB with DPD and rifampicin 1 (ChIP-exo)
91 - SoxS PQ 2
92 - SoxS PQ 1
93 - EC18n178 RpoH 2.5 min Time course 1
94 - Wild type control (20 min)
95 - pT7_ChIPSeq_1
96 - pT7_ChIPSeq_2
97 - EC18n182 RpoH 0 min Time course 3
98 - RNAP old rep1
99 - Lrp_Leu_1
100 - Lrp_Leu_3
101 - Lrp_Leu_2
102 - RpoB with DPD 1 (ChIP-exo)
103 - Cra acetate 1
104 - Cra acetate 2
105 - EC18n171 RpoH 20 min Time course 2
106 - EC18n179 RpoH 5 min Time course 1
107 - Ptac::fnr - A - 16 µM IPTG
108 - ∆fur ∆ryhB Aerobic B
109 - Nac_RNASeq
110 - LB 2.0 B1 TEX pos L1 GA
111 - ∆fur Anaerobic A
112 - σ32 30°C short RNase
113 - EC18n181 RpoH 20 min Time course 1
114 - M63 0.4 B2 TEX neg L1 HS1
115 - M63 0.4 B2 TEX neg L1 HS2
116 - EC18n168 RpoH 2.5 min Time course 2
117 - Δcra glucose 1
118 - Δcra glucose 2
119 - Lrp_NH4Cl_2
120 - Lrp_NH4Cl_3
121 - Lrp_NH4Cl_1
122 - LB 2.0 B1 TEX neg L2 HS2
123 - ΔsoxS PQ 1
124 - Δcra fructose 1
125 - Δcra fructose 2
126 - WT_RNASeq
127 - WT glucose 1
128 - WT glucose 2
129 - Wild type control (5 min)
130 - EC18n184 RpoH 5 min Time course 3
131 - Fur IP ChIP-Seq Aerobic C
132 - RpoB with Fe and rifampicin 1 (ChIP-exo)
133 - Fur with Fe 2 (ChIP-exo)
134 - FNR - Anaerobic - A
135 - WT with Fe 1 (RNA-seq)
136 - FNR - Anaerobic - C
137 - FNR - Anaerobic - B
138 - ΔompR NaCl 2
139 - ΔompR NaCl 1
140 - Ecoli_dFNR_rep1_anaerobic
141 - Ptac::fnr - A - 4 µM IPTG
142 - LB 2.0 B2 TEX neg L2 HS2
143 - PurR_Adenine_1
144 - Ecoli_wild-type_rep1_anaerobic
145 - EC18n167 RpoH 0 min Time course 2
146 - Wild-type Anaerobic B
147 - Fur with Fe 1 (ChIP-exo)
148 - FNR - ∆hns∆stpA A
149 - RpoB with Fe 2 (ChIP-exo)
150 - FNR - ∆hns∆stpA B
151 - RpoB ∆cra 2
152 - RpoB with DPD and rifampicin 2 (ChIP-exo)
153 - RpoB ∆cra 1
154 - WT NaCl 1
155 - WT NaCl 2
156 - WT with DPD 1 (RNA-seq)
157 - LB 0.4 B1 TEX neg L1 GA
158 - Ptac::fnr - B - 8 µM IPTG
159 - ArgR_Arginine_2
160 - LB 0.4 B2 TEX neg L1 HS2
161 - LB 0.4 B2 TEX neg L1 HS1
162 - ArgR_Arginine_1
163 - ArgR_NH4Cl_1
164 - Escherichia coli str. K-12 substr. MG1655
165 - OxyR PQ 1
166 - ΔgadX pH5.5 2
167 - ∆fur ∆ryhB Anaerobic A
168 - ΔgadX pH5.5 1
169 - Fur IP ChIP-Seq Anaerobic, Iron Deficient B
170 - Δfur with Fe 1 (RNA-seq)
171 - Fur IP ChIP-Seq Anaerobic, Iron Deficient A
172 - ß - Anaerobic - A
173 - ß - Anaerobic - B
174 - σ32 ChIP DNA, control
175 - SeqA new deltaSeqA
176 - M63 0.4 B1 TEX neg L1 GA
177 - TrpR_Trp
178 - Ptac::fnr - B - 16 µM IPTG
179 - ß - Aerobic - A
180 - Ptac::fnr - B - 4 µM IPTG
181 - ß - Aerobic - B
182 - EC18n177 RpoH 0 min Time course 1
183 - σ32 43°C short RNase
184 - ∆ryhB Anaerobic
185 - Input ChIP-Seq
186 - Δfur with DPD 1 (RNA-seq)
187 - RpoH induced (5 min)
188 - ∆fur Anaerobic B
189 - FNR - Anaerobic - Affinity Purified - B
190 - EC18n186 RpoH 20 min Time course 3
191 - FNR - Anaerobic - Affinity Purified - A
192 - ChIP-exo RpoS pH5.5 2
193 - RpoB with DPD 2 (ChIP-exo)
194 - ChIP-exo RpoS pH5.5 1
195 - ΔsoxR PQ 2
196 - PurR_Adenine_2
197 - Ptac::fnr - C - 16 µM IPTG
198 - WT PQ 1
199 - EC18n170 RpoH 10 min Time course 2
200 - ∆fur ∆ryhB Anaerobic B
201 - M63 0.4 B1 TEX pos L1 GA
202 - RpoH induced (10 min)
203 - Wild-type Anaerobic A
204 - ArgR_NH4Cl_2
205 - LB 2.0 B1 TEX neg L1 GA
206 - WT with DPD 2 (RNA-seq)
207 - ∆fur Anaerobic [IP vs nput]
208 - EC18n183 RpoH 2.5 min Time course 3
209 - ∆fur ∆ryhB Aerobic A
210 - RpoB ∆crp 2
211 - NtrC_ChIPSeq
212 - RpoB ∆crp 1
213 - WT fructose 1
214 - ΔgadE pH5.5 2
215 - ΔgadE pH5.5 1
216 - WT fructose 2
217 - OmpR_ChIPSeq
218 - RpoB with Fe and rifampicin 2 (ChIP-exo)
219 - WT pH5.5 1
220 - WT pH5.5 2
221 - Wild type control (2.5 min)
222 - Ecoli_dFNR_rep2_anaerobic
223 - Fur with DPD 1 (ChIP-exo)
224 - ∆fur Aerobic A
225 - ∆fur Aerobic B
226 - ΔsoxS PQ 2
227 - Δfur with DPD 2 (RNA-seq)
228 - Fur with DPD 2 (ChIP-exo)
229 - SeqA old rep1
230 - LB 2.0 B2 TEX pos L2 HS2