| Strain, strain background (Escherichia coli) |
G78 trmD-deg
|
This paper |
|
TrmD is fused with a C-terminal YALAA degron tag |
| Strain, strain background (Escherichia coli) |
G78 trmD-cont
|
This paper |
|
Control strain without a degron tag |
| Strain, strain background (Escherichia coli) |
MG1655 trmD-KO
|
Masuda et al., 2019
|
|
|
| Strain, strain background (Escherichia coli) |
MG1655 trmD-KO ilvL Ala-Ala mutant |
This paper |
|
CRISPR mutant possessing GCA-GCG codons replacing CCA-CCG codons on ilvL gene |
| Strain, strain background (Escherichia coli) |
JM109 trmD-KO
|
Demo et al., 2021
|
|
|
| Strain, strain background (Escherichia coli) |
BL21(DE3) trmD-KO
|
Gamper et al., 2015a
|
|
|
| Strain, strain background (Escherichia coli) |
BL21(DE3) |
CGSC |
CGSC#: 12504 |
|
| Antibody |
anti-TrmD (Rabbit polyclonal) |
Li and Björk, 1999 doi: 10.1017/S1355838299980834
|
|
WB (1:10000) |
| Antibody |
anti-rabbit IgG (Goat polyclonal) |
Sigma-Aldrich |
Cat#: A0545 |
WB(1:160000) |
| Peptide, recombinant protein |
Proteinase K |
Promega |
Cat#: V302B |
|
| Peptide, recombinant protein |
Micrococcal nuclease |
Roche |
Cat#: 10107921001 |
|
| Peptide, recombinant protein |
Superscript III reverse transcriptase |
Invitrogen |
Cat#: 18080–044 |
|
| Peptide, recombinant protein |
RQ1 RNase-free DNase |
Promega |
Cat#: M6101 |
|
| Commercial assay or kit |
TruSeq Stranded Total RNA kit |
Illumina |
Cat#: 20020598 |
|
| Commercial assay or kit |
SuperSignal West Pico Chemiluminescent Substrate |
Thermo Fisher Scientific |
Cat#: 34080 |
|
| Commercial assay or kit |
NEBuilder HiFi DNA Assembly Cloning Kit |
New England Biolabs |
Cat#: E5520S |
|
| Commercial assay or kit |
Nano-Glo Luciferase Assay System |
Promega |
Cat#: N1110 |
|
| Commercial assay or kit |
TRIzol |
Invitrogen |
Cat#: 15596026 |
|
| Commercial assay or kit |
Direct-zol RNA MiniPrep Kits |
Zymo Research |
Cat#: R2051 |
|
| Commercial assay or kit |
RevertAid First Strand cDNA synthesis Kit |
Thermo Fisher Scientific |
Cat#: K1622 |
|
| Commercial assay or kit |
SYBR Green I Master |
Roche |
Cat#: 04707516001 |
|
| Software, algorithm |
Skewer |
Jiang et al., 2014
|
|
|
| Software, algorithm |
bowtie |
Langmead et al., 2009
|
|
|
| Software, algorithm |
DESeq |
Love et al., 2014
|
|
|
| Software, algorithm |
Xtail |
Xiao et al., 2016
|
|
|
| Software, algorithm |
DAVID |
Huang et al., 2007
|
|
|
| Software, algorithm |
Pathway Tools |
Karp et al., 2021
|
|
|
| Software, algorithm |
ImageQuant |
GE Healthcare |
|
|
| Software, algorithm |
Kaleidagraph |
Synergy software |
|
|
| Software, algorithm |
ImageJ |
NIH |
|
|
| Other |
MOPS EZ Rich Defined |
Teknova |
Cat#: M2105 |
Growth medium |
