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David BIKARD
badSeed_public
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8648e507
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8648e507
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6 years ago
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David Bikard
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8648e507
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@@ -4,7 +4,7 @@ This repository contains the code used in the paper:
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@@ -4,7 +4,7 @@ This repository contains the code used in the paper:
Lun Cui, Antoine Vigouroux, Francois Rousset, Hugo Varet, Varun Khanna & David Bikard
Lun Cui, Antoine Vigouroux, Francois Rousset, Hugo Varet, Varun Khanna & David Bikard
In this study we designed a library of
84215 unique
guide RNAs targeting random positions
In this study we designed a library of guide RNAs targeting random positions
along the genome of E. coli MG1655, with the simple requirement of a “NGG” PAM. The library
along the genome of E. coli MG1655, with the simple requirement of a “NGG” PAM. The library
contains an average of 19 targets per gene. A pool of guide RNAs obtained through on-chip
contains an average of 19 targets per gene. A pool of guide RNAs obtained through on-chip
oligo synthesis was cloned under the control of a constitutive promoter on plasmid psgRNA
oligo synthesis was cloned under the control of a constitutive promoter on plasmid psgRNA
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@@ -14,7 +14,7 @@ over 17 generations with anhydrotetracycline (aTc). The effect of each guide on
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@@ -14,7 +14,7 @@ over 17 generations with anhydrotetracycline (aTc). The effect of each guide on
the fold change in abundance (log2FC) of the guide RNA in the library
the fold change in abundance (log2FC) of the guide RNA in the library
during the course of the experiment, as measured through deep sequencing of the library.
during the course of the experiment, as measured through deep sequencing of the library.
The log2FC data for all guides in the screen can be found in the file
Supplementary_table_6-
screen_data.csv
The log2FC data for all guides in the screen can be found in the file screen_data.csv
The analysis is divided in three jupyter notebooks:
The analysis is divided in three jupyter notebooks:
*
Effect of dCas9 binding position and orientation.ipynb
*
Effect of dCas9 binding position and orientation.ipynb
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