updating readme

README.md

@@ -26,6 +26,9 @@ experimental_conditions:
   media:
     # Mahendrawada et al 2025: "synthetic complete (SC) media"
     name: synthetic_complete
+    carbon_source:
+      # Carbon source is not specified in the paper; D-glucose is standard for SC media.
+      - compound: D-glucose
     nitrogen_source:
       - compound: yeast_nitrogen_base
         # Mahendrawada et al 2025: 1.7 g/L (without ammonium sulfate or amino acids (BD Difco))
@@ -1200,6 +1203,67 @@ configs:
           names: ["standard_30C", "SM", "galactose", "raffinose", "heat_shock_37C"]
       description: Environmental growth condition for this experiment
       role: experimental_condition
+      definitions:
+        standard_30C:
+          description: Standard synthetic complete medium at 30°C; the baseline growth condition.
+          temperature_celsius: 30
+          media:
+            name: synthetic_complete
+        SM:
+          description: >-
+            Amino acid starvation induced by sulfometuron methyl (SM) in
+            synthetic complete medium lacking Ile/Val.
+          temperature_celsius: 30
+          media:
+            name: synthetic_complete_minus_ile_val
+          chemical_treatment:
+            compound: sulfometuron_methyl
+            concentration_ug_per_mL: 0.5
+            duration_minutes: 60
+        galactose:
+          description: >-
+            Galactose induction condition for Gal4 experiments; cells grown
+            in YEP-Raffinose then induced with 2% galactose for 2 hours.
+          temperature_celsius: 30
+          media:
+            # Methods: YEP-Raffinose (1% yeast extract, 2% peptone, 2% raffinose)
+            # induced with 2% galactose for 2h
+            name: yeast_extract_peptone_raffinose_plus_galactose
+            carbon_source:
+              - compound: D-raffinose
+                concentration_percent: 2
+              - compound: D-galactose
+                concentration_percent: 2
+            nitrogen_source:
+              - compound: yeast_extract
+                concentration_percent: 1
+              - compound: peptone
+                concentration_percent: 2
+          galactose_induction_duration_hours: 2
+        raffinose:
+          description: >-
+            Uninduced raffinose condition for Gal4 experiments; cells grown
+            in YEP-Raffinose without galactose addition.
+          temperature_celsius: 30
+          media:
+            # Methods: YEP-Raffinose (1% yeast extract, 2% peptone, 2% raffinose)
+            name: yeast_extract_peptone_raffinose
+            carbon_source:
+              - compound: D-raffinose
+                concentration_percent: 2
+            nitrogen_source:
+              - compound: yeast_extract
+                concentration_percent: 1
+              - compound: peptone
+                concentration_percent: 2
+        heat_shock_37C:
+          description: >-
+            Heat shock to 37°C for 10 minutes, used for Hsf1 and Msn2
+            experiments; equal volume of 44°C medium added to 30°C culture.
+          initial_temperature_celsius: 30
+          mixing_temperature_celsius: 44
+          final_temperature_celsius: 37
+          incubation_duration_minutes: 10
     - name: timepoint
       dtype: float64
       description: Time point in minutes (standard is 30 minutes post-treatment. very few other timepoints)
@@ -1273,6 +1337,16 @@ configs:
           names: ["DMSO", "IAA"]
       description: Degron treatment condition (DMSO control or IAA degradation)
       role: experimental_condition
+      definitions:
+        DMSO:
+          description: DMSO vehicle control; the auxin-inducible degron tag is inactive and the transcription factor is present.
+        IAA:
+          description: Indole-3-acetic acid (auxin) treatment to induce degradation of the IAA7-tagged transcription factor.
+          chemical_treatment:
+            compound: indole-3-acetic_acid
+            # Methods: 500 μM IAA for 30 min
+            concentration_uM: 500
+            duration_minutes: 30
     - name: degron_variant
       dtype:
         class_label:
@@ -1284,6 +1358,53 @@ configs:
           names: ["standard_30C", "SM", "galactose", "raffinose", "heat_shock_37C"]
       description: Environmental growth condition
       role: experimental_condition
+      definitions:
+        standard_30C:
+          description: Standard synthetic complete medium at 30°C; the baseline growth condition.
+          temperature_celsius: 30
+          media:
+            name: synthetic_complete
+        SM:
+          description: >-
+            Amino acid starvation induced by sulfometuron methyl (SM) in
+            synthetic complete medium lacking Ile/Val.
+          temperature_celsius: 30
+          media:
+            name: synthetic_complete_minus_ile_val
+          chemical_treatment:
+            compound: sulfometuron_methyl
+            concentration_ug_per_mL: 0.5
+            duration_minutes: 60
+        galactose:
+          description: >-
+            Galactose induction condition for Gal4 experiments; cells grown in
+            YEP-Raffinose then induced with 2% galactose for 2 hours.
+          temperature_celsius: 30
+          media:
+            name: yeast_extract_peptone
+            carbon_source:
+              - compound: D-raffinose
+                concentration_percent: 2
+              - compound: D-galactose
+                concentration_percent: 2
+          galactose_induction_duration_hours: 2
+        raffinose:
+          description: >-
+            Uninduced raffinose condition for Gal4 experiments; cells grown in
+            YEP-Raffinose without galactose addition.
+          temperature_celsius: 30
+          media:
+            name: yeast_extract_peptone
+            carbon_source:
+              - compound: D-raffinose
+                concentration_percent: 2
+        heat_shock_37C:
+          description: >-
+            Heat shock to 37°C for 10 minutes, used for Hsf1 and Msn2
+            experiments; equal volume of 44°C medium added to 30°C culture.
+          initial_temperature_celsius: 30
+          final_temperature_celsius: 37
+          incubation_duration_minutes: 10
     - name: timepoint
       dtype: float64
       description: Time point for time-series experiments (minutes)
@@ -1364,6 +1485,53 @@ configs:
           names: ["standard_30C", "SM", "galactose", "raffinose", "heat_shock_37C"]
       description: Environmental growth condition
       role: experimental_condition
+      definitions:
+        standard_30C:
+          description: Standard synthetic complete medium at 30°C; the baseline growth condition.
+          temperature_celsius: 30
+          media:
+            name: synthetic_complete
+        SM:
+          description: >-
+            Amino acid starvation induced by sulfometuron methyl (SM) in
+            synthetic complete medium lacking Ile/Val.
+          temperature_celsius: 30
+          media:
+            name: synthetic_complete_minus_ile_val
+          chemical_treatment:
+            compound: sulfometuron_methyl
+            concentration_ug_per_mL: 0.5
+            duration_minutes: 60
+        galactose:
+          description: >-
+            Galactose induction condition for Gal4 experiments; cells grown in
+            YEP-Raffinose then induced with 2% galactose for 2 hours.
+          temperature_celsius: 30
+          media:
+            name: yeast_extract_peptone
+            carbon_source:
+              - compound: D-raffinose
+                concentration_percent: 2
+              - compound: D-galactose
+                concentration_percent: 2
+          galactose_induction_duration_hours: 2
+        raffinose:
+          description: >-
+            Uninduced raffinose condition for Gal4 experiments; cells grown in
+            YEP-Raffinose without galactose addition.
+          temperature_celsius: 30
+          media:
+            name: yeast_extract_peptone
+            carbon_source:
+              - compound: D-raffinose
+                concentration_percent: 2
+        heat_shock_37C:
+          description: >-
+            Heat shock to 37°C for 10 minutes, used for Hsf1 and Msn2
+            experiments; equal volume of 44°C medium added to 30°C culture.
+          initial_temperature_celsius: 30
+          final_temperature_celsius: 37
+          incubation_duration_minutes: 10
     - name: replicate
       dtype: string
       description: Biological replicate identifier (A, B, or C)
@@ -1433,6 +1601,53 @@ configs:
           names: ["standard_30C", "SM", "galactose", "raffinose", "heat_shock_37C"]
       description: Environmental growth condition
       role: experimental_condition
+      definitions:
+        standard_30C:
+          description: Standard synthetic complete medium at 30°C; the baseline growth condition.
+          temperature_celsius: 30
+          media:
+            name: synthetic_complete
+        SM:
+          description: >-
+            Amino acid starvation induced by sulfometuron methyl (SM) in
+            synthetic complete medium lacking Ile/Val.
+          temperature_celsius: 30
+          media:
+            name: synthetic_complete_minus_ile_val
+          chemical_treatment:
+            compound: sulfometuron_methyl
+            concentration_ug_per_mL: 0.5
+            duration_minutes: 60
+        galactose:
+          description: >-
+            Galactose induction condition for Gal4 experiments; cells grown in
+            YEP-Raffinose then induced with 2% galactose for 2 hours.
+          temperature_celsius: 30
+          media:
+            name: yeast_extract_peptone
+            carbon_source:
+              - compound: D-raffinose
+                concentration_percent: 2
+              - compound: D-galactose
+                concentration_percent: 2
+          galactose_induction_duration_hours: 2
+        raffinose:
+          description: >-
+            Uninduced raffinose condition for Gal4 experiments; cells grown in
+            YEP-Raffinose without galactose addition.
+          temperature_celsius: 30
+          media:
+            name: yeast_extract_peptone
+            carbon_source:
+              - compound: D-raffinose
+                concentration_percent: 2
+        heat_shock_37C:
+          description: >-
+            Heat shock to 37°C for 10 minutes, used for Hsf1 and Msn2
+            experiments; equal volume of 44°C medium added to 30°C culture.
+          initial_temperature_celsius: 30
+          final_temperature_celsius: 37
+          incubation_duration_minutes: 10
     - name: replicate
       dtype: string
       description: Biological replicate identifier (A, B, or C)
@@ -1502,6 +1717,16 @@ configs:
           names: ["DMSO", "IAA"]
       description: Degron treatment condition (DMSO control or IAA degradation)
       role: experimental_condition
+      definitions:
+        DMSO:
+          description: DMSO vehicle control; the auxin-inducible degron tag is inactive and the transcription factor is present.
+        IAA:
+          description: Indole-3-acetic acid (auxin) treatment to induce degradation of the IAA7-tagged transcription factor.
+          chemical_treatment:
+            compound: indole-3-acetic_acid
+            # Methods: 500 μM IAA for 30 min
+            concentration_uM: 500
+            duration_minutes: 30
     - name: replicate
       dtype: string
       description: Biological replicate identifier (A, B, or C)

scripts/parse_mahendrawada_data.R

@@ -90,3 +90,37 @@ gc()
 #     write_statistics = TRUE,
 #     use_dictionary = c(
 #         chr = TRUE))
+
+##### separating GAL4 samples
+
+mahendrawada_chec_af_combined <- list(
+   meta = arrow::read_parquet("~/code/hf/mahendrawada_2025/chec_mahendrawada_m2025_af_combined_meta.parquet"),
+   data = arrow::read_parquet("~/code/hf/mahendrawada_2025/chec_mahendrawada_m2025_af_combined.parquet")
+)
+
+
+
+standard_meta = mahendrawada_chec_af_combined$meta |>
+    filter(condition=='standard')
+
+standard_data = mahendrawada_chec_af_combined$data |>
+    filter(sample_id %in% standard_meta$sample_id) |>
+    left_join(dplyr::select(standard_meta,
+                            sample_id,
+                            regulator_locus_tag,
+                            regulator_symbol,
+                            mahendrawada_symbol)) |>
+    dplyr::relocate(sample_id,
+                    regulator_locus_tag,
+                    regulator_symbol,
+                    mahendrawada_symbol)
+
+
+# arrow::write_parquet(
+#     standard_data,
+#     "~/code/hf/mahendrawada_2025/chec_mahendrawada_m2025_af_combined_standard.parquet",
+#     compression = "zstd",
+#     compression_level = 3
+# )
+
+