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EXPERIMENTAL JOURNAL PHD

Experimental progress 🥼 🦠

General docs

1. Balance of the 2021
3. Balance of the 2020
4. Balance of the 2019 and outlook to the 2020
5. Title: Yearly Progress Meeting (Starting my 3rd PhD year)

Protocols and Strains

YPD media
High efficiency Yeast Transformation
Yeast DAPI Staining
Strain construction database :snail:

Experimental journal-11-2022

6. Title : how do yeast cells look like during log phase at different galactose concentrations? (2nd experiment)

Experimental journal-10-2022

7. Title : do yeast cells show multinuclei upon CDC42 depletion? (experiment)
8. Title : how do yeast cells look like during log phase at different galactose concentrations? (experiment)

Experimental journal-09-2022

9. Title : do yeast cells show multinuclei upon CDC42 depletion? (test)

Experimental journal-10-2021

10. Title : Genetic checks for a single colony from the stock of bem1:KanMx mutants

Experimental journal-09-2021

11. Title : Biotek round on new gal concentrations at 36C
12. Title : Biotek volume reduced during incubation at 30C to check supressors
13. Title : Genetic checks for the Gal strains used in the Biotek

Experimental journal-08-2021

14. Title: Biotek to test ylic140 dbem3dbem1pGal strain
15. Title: Transformation/checking on ylic136 and ylic138 with bem1::KANMX
16. Title: Biotek 30C with new Gal concentration below 0.1%

Experimental journal-06-2021

17. Title : Contruction dbem1dbem3+pGal from ylic139 -> ylic140

Experimental journal-05-2021

18. Title: Biotek - 1st experiment for paper all strains

Experimental journal-04-2021

19. Title : “Biotek experiment for new dbem1 pGal-cdc42 strain”

Experimental journal-03-2021

20. Title : Genomic extraction and PCR of clean ylic137_2
21. Title: Transformation on nrp1::HYGRO with bem1::KANMX
22. Title : bem1::KanMX transformation in WT+pGal-CDC42

Experimental journal-02-2021

23. Title : Genomic extractions,PCR for checking and sequencing of dbem3 and dbem3dnrp1 new strains

Experimental journal-01-2021

24. Title : PCR and sequencing checks for the new strains dbem3 and dbem3dnrp1
25. Title: Supp controls on sfgFP influence on the bulk growth

Experimental journal-12-2020

26. Title: ylic133 and ylic136 transformation with bem3d::NAT
27. Samples

Experimental journal-11-2020

28. Title : gDNA extraction from yWT04a
29. Title : gDNA extraction of yll138

Experimental journal-10-2020

30. Title : Digestion and Ligation for sequencing
31. Title : Digestion and Ligation Test for new SATAY DNA
32. Title: More DNA extraction of dnrp1 and WT strains
33. Title : ylic133 and ylic136 transformation with bem3d::NAT

Experimental journal-08-2020

34. Title: Towards DNA sequencing: Digestion, Circularization and PCR of the transposon-genome junctions.
35. DNA extraction from SATAY samples
36. Title : 20200810-SATAY for \(\Delta\) bem2, \(\Delta\) nrp1 and WT

Experimental journal-07-2020

37. Title : Transformation of ylic133 (WT ade- ura-) with pbK549 for SATAY
38. Title : Transformation of ylic135 and ylic136 with pbK549 for further SATAY experiment
39. Title : Preparation for PCR check of BEM2 presence and absence in strain ylic135

Experimental journal-06-2020

40. Title : How different are the number of interactors of essential genes compared with non essential genes.
41. Date

Experimental journal-04-2020

45. Title: Checking bem2 deletion on the transformed strain ylic133_5
46. Title : From common properties to Synthetic Lethality prediction
47. Title: 24042020-Plan for next experiments
48. Title: 23042020-Summary on machine learning study
49. Date

Experimental journal-03-2020

52. Title : 20200305-FACs experiment with strains ywkd065, ywkd024, ywkd038 and ywkd001

Experimental journal-02-2020

53. Title : 20200227-FACs experiment with strains ywkd065, ywkd024, ywkd038 and ywkd001
54. Title: Transformation of ylic133_5 with the PCR products from yll137 and yll140
55. Title :What are the output channels from flow cytometry actualling telling us about the fluorescence of every cell?
56. Title : Comparison between the fAcs settings used for Werner in 2017 with the ones I am using currently.
57. Title : Design of the genomic transformation to make dnrp1 and dbem2 strains usable for SATAY

Experimental journal-01-2020

58. Title: FACs experiment with the same conditions as the microscopy done to quantify the cell sizes for the pAl1-Cdc42-sfGFP strains (III).
59. Title: FACs experiment with the same conditions as the microscopy done to quantify the cell sizes for the pGAl1-Cdc42-sfGFP strains (II).
60. Title: FACs experiment with the same conditions as the microscopy done to quantify the cell sizes for the pAl1-Cdc42-sfGFP strains. (I)
61. Title: Machine learning projects proposal for MsC/BsC/internships
62. Title:14012020-Mapping essential genes in WT and getting insights from it.

Experimental journal-10-2019

63. Title: 09102019- Sanity check of transformants ylic133+pBk549, Byk832+pBk549 to know if they suitable for SATAY. :smile:
64. Title: 03102019- III pBK549 transformation on ylic133 for further sanity check in SATAY :blush: :punch:
65. Title : 01102019- II pBK549 transformation on ylic133 for further sanity check in SATAY :pensive:

Experimental journal-09-2019

66. Title : 24092019-Mating of ylic134 with yEK7a :broken_heart:
67. Title : 24092019- pBK549 transformation on ylic133 for further sanity check in SATAY. :pensive:
68. Title : 12092019-Transformation of ylic133 with the pLL112 plasmid :pensive:

Experimental journal-08-2019

69. Title: 27082019-Sporulation protocol of 8 re-streakings from ylic133_5+yEk7a :pensive:
70. Title: 22082019 Mating using liquid drops of yEK7a and ylic133_5 :broken_heart:
71. Title : 16082019 Script for the visualization of the correlation between number of common interactions and type of interactions
72. Title : 12082019-Checking clones of Byk832 and ylic33_1 for SATAY :ok:
73. Title : 07082019-Crossing of yEK7a with ylic133_1 :broken_heart: :pensive:
74. Title: 05082019-Byk832 transformation with pBk549 :ok: :white_check_mark:

Experimental journal-07-2019

75. Title: 31072019 Double check Byk832T biolog. replicates suitability for SATAY.
76. Title : 24072019-Strategies to generate the strains I want to study using SATAY :page_with_curl:
78. Title: 29072019-SATAY 1st attempt with Byk832-T :pray: :confused: :x:
79. Title : 23072019-Glycerols stocks of ylic133 biological replicates :snowflake:
80. Title: 22072019-Sequencing of ylic133 biological replicates :ok: :white_check_mark:
81. Title : 17072019-DNA extraction of ylic133: ura3- ade2- clones anad PCR :ok: :white_check_mark:
82. Title : 15072019-Check of growth in -ade and -ura of 10 clones of Byk832+pbk549 :ok:
83. 16-07-2019-Script in python to find the most connected genes to a query gene. :milky_way:
86. Title : 11072019-ylic132-1 and ylic132-2 transformation with the OEP2 :white_check_mark:
88. Title : 10072019-Byk832 transformation using pBK549 plasmid (:ok:)
89. Title: 26062019-Sequencing of the URA integration in ade2 locus in ylic132 :ok: :white_check_mark:
90. Title : 03072019-Digestion pattern of pBK549 (Succesful) :ok:

Experimental journal-06-2019

91. Title: 26062019-ylic132 transformation with the OEP2 (unsuccesful) :x: :disappointed:
92. Title: 26062019-Sequencing of the URA integration in ade2 locus in ylic132 :white_check_mark:
93. Title: 25062019-Experimental Card about the SATAY experiment
94. Title: 19062019-Byk832 (ETH strain) transformation with pbK549 (very low effciency) :pensive: :confused:
95. Title: 14062019-ylic132 transformation with the OEP2 (unsuccesful) :x: :disappointed:
96. Title: 06062019-Yeast transformation with the OEP1 :white_check_mark: :white_check_mark:
97. Title: 03062019-Design of new primers, for the right homology arm, for transformation that avoid the overlap with the RGA1 gene.
98. Title: 03062019-Sequencing the homology arms of yll3a strain around the ade2 gene :ok:.

Experimental journal-05-2019

99. Title: URA transformation in ADE2 locus

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High efficiency Yeast Transformation

High efficiency Yeast Transformation#

By Leila Iñigo de la Cruz
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