stationary phase e coli cells  (New England Biolabs)


Bioz Verified Symbol New England Biolabs is a verified supplier
Bioz Manufacturer Symbol New England Biolabs manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
    • 99
    Name:
    Nuclease free Water
    Description:
    Nuclease free Water 100 ml
    Catalog Number:
    B1500L
    Price:
    62
    Category:
    Ribonuclease Protection Assays
    Size:
    100 ml
    		Buy from Supplier

    Structured Review

    New England Biolabs stationary phase e coli cells
    Nuclease free Water
    Nuclease free Water 100 ml
    https://www.bioz.com/result/stationary phase e coli cells/product/New England Biolabs
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    stationary phase e coli cells - by Bioz Stars, 2021-05
    99/100 stars

    Images

    1) Product Images from "Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli"

    Article Title: Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli

    Journal: bioRxiv

    doi: 10.1101/2021.04.06.438613

    Distributions of 5′-end sequences for RNAs generated in primer-independent initiation and primer-dependent initiation in vivo and in vitro . A. lac CONS-N10 library. Base pairs in the N10 region are numbered based on their position relative to the promoter −10 element. Colors as in Figure 1B . B-C. RNA 5′-end distribution histograms (mean ± SD, N = 3) for RNAs generated by primer-independent initiation (top) or primer-dependent initiation (bottom) in stationary-phase E. coli cells (panel B) or in vitro , with the dinucleotide primer UpA (panel C). Dashed line indicates the mean 5′-end position (mean ± SD, N = 3).
    Figure Legend Snippet: Distributions of 5′-end sequences for RNAs generated in primer-independent initiation and primer-dependent initiation in vivo and in vitro . A. lac CONS-N10 library. Base pairs in the N10 region are numbered based on their position relative to the promoter −10 element. Colors as in Figure 1B . B-C. RNA 5′-end distribution histograms (mean ± SD, N = 3) for RNAs generated by primer-independent initiation (top) or primer-dependent initiation (bottom) in stationary-phase E. coli cells (panel B) or in vitro , with the dinucleotide primer UpA (panel C). Dashed line indicates the mean 5′-end position (mean ± SD, N = 3).

    Techniques Used: Generated, In Vivo, In Vitro

    Promoter-sequence dependence of primer-dependent initiation in vivo : sequences flanking the primer binding site Sequence logo ( 35 ) for primer-dependent initiation in stationary-phase E. coli cells with each of the 16 dinucleotides at TSS positions 7, 8, and 9 (corresponding to primer binding sites 6-7, 7-8, and 8-9, respectively). The height of each base “X” at each position “Y” represents the log 2 average of the % 5′-OH RNAs computed across sequences containing nontemplate-strand X at position Y. Red, consensus nucleotides; black, non-consensus nucleotides. Gray box indicates positions where enrichment values could not be computed.
    Figure Legend Snippet: Promoter-sequence dependence of primer-dependent initiation in vivo : sequences flanking the primer binding site Sequence logo ( 35 ) for primer-dependent initiation in stationary-phase E. coli cells with each of the 16 dinucleotides at TSS positions 7, 8, and 9 (corresponding to primer binding sites 6-7, 7-8, and 8-9, respectively). The height of each base “X” at each position “Y” represents the log 2 average of the % 5′-OH RNAs computed across sequences containing nontemplate-strand X at position Y. Red, consensus nucleotides; black, non-consensus nucleotides. Gray box indicates positions where enrichment values could not be computed.

    Techniques Used: Sequencing, In Vivo, Binding Assay

    Promoter-sequence dependence of primer-dependent initiation: primer binding site. A. Relative usage of dinucleotides in primer-dependent initiation in stationary-phase E. coli cells. Values represent the percentage of total 5′-OH RNAs generated using each of the 16 dinucleotide primers (mean, N = 3). Bold, dinucleotides preferentially used as primers. B. Complementarity between the primer binding site and dinucleotide in primer-dependent initiation. Top: primer-dependent initiation involving template-strand complementarity to both 5′ and 3′ nucleotides of primer (TSS-1, TSS), template-strand complementarity to only 3′ nucleotide of primer (TSS), template-strand complementarity to only 5′ nucleotide of primer (TSS-1), or no template-strand complementarity to primer (none). Three vertical lines, complementarity; X, non-complementarity. Other symbols and colors as in Figure 1 . Bottom: percentage of primer-dependent initiation involving complementarity to both 5′ and 3′ nucleotides of primer (TSS-1, TSS; pink), complementarity to only 3′ nucleotide of primer (TSS; purple), or template-strand complementarity to only 5′ nucleotide of primer or no template-strand complementarity to primer (TSS-1 or none; white) in stationary-phase E. coli cells (left) or in vitro , with the dinucleotide primer UpA (right) (mean ± SD, N = 3).
    Figure Legend Snippet: Promoter-sequence dependence of primer-dependent initiation: primer binding site. A. Relative usage of dinucleotides in primer-dependent initiation in stationary-phase E. coli cells. Values represent the percentage of total 5′-OH RNAs generated using each of the 16 dinucleotide primers (mean, N = 3). Bold, dinucleotides preferentially used as primers. B. Complementarity between the primer binding site and dinucleotide in primer-dependent initiation. Top: primer-dependent initiation involving template-strand complementarity to both 5′ and 3′ nucleotides of primer (TSS-1, TSS), template-strand complementarity to only 3′ nucleotide of primer (TSS), template-strand complementarity to only 5′ nucleotide of primer (TSS-1), or no template-strand complementarity to primer (none). Three vertical lines, complementarity; X, non-complementarity. Other symbols and colors as in Figure 1 . Bottom: percentage of primer-dependent initiation involving complementarity to both 5′ and 3′ nucleotides of primer (TSS-1, TSS; pink), complementarity to only 3′ nucleotide of primer (TSS; purple), or template-strand complementarity to only 5′ nucleotide of primer or no template-strand complementarity to primer (TSS-1 or none; white) in stationary-phase E. coli cells (left) or in vitro , with the dinucleotide primer UpA (right) (mean ± SD, N = 3).

    Techniques Used: Sequencing, Binding Assay, Generated, In Vitro

    Promoter-sequence dependence of primer-dependent initiation in stationary-phase E. coli cells: primer binding site Top: primer-dependent initiation involving template-strand complementarity to both 5′ and 3′ nucleotides of primer (TSS-1, TSS), template-strand complementarity to only 3′ nucleotide of primer (TSS), template-strand complementarity to only 5′ nucleotide of primer (TSS-1), or no template-strand complementarity to primer (none). Three vertical lines, complementarity; X, non-complementarity. Other symbols and colors as in Figure 1 . Bottom: percentage of primer-dependent initiation involving complementarity to both 5′ and 3′ nucleotides of primer (TSS-1, TSS; pink), complementarity to only 3′ nucleotide of primer (TSS; purple), or template-strand complementarity to only 5′ nucleotide of primer or no template-strand complementarity to primer (TSS-1 or none; white) in stationary-phase E. coli cells for primer binding sites located 6-7, 7-8, or 8-9 base pairs downstream of the promoter −10 element (mean ± SD, N = 3).
    Figure Legend Snippet: Promoter-sequence dependence of primer-dependent initiation in stationary-phase E. coli cells: primer binding site Top: primer-dependent initiation involving template-strand complementarity to both 5′ and 3′ nucleotides of primer (TSS-1, TSS), template-strand complementarity to only 3′ nucleotide of primer (TSS), template-strand complementarity to only 5′ nucleotide of primer (TSS-1), or no template-strand complementarity to primer (none). Three vertical lines, complementarity; X, non-complementarity. Other symbols and colors as in Figure 1 . Bottom: percentage of primer-dependent initiation involving complementarity to both 5′ and 3′ nucleotides of primer (TSS-1, TSS; pink), complementarity to only 3′ nucleotide of primer (TSS; purple), or template-strand complementarity to only 5′ nucleotide of primer or no template-strand complementarity to primer (TSS-1 or none; white) in stationary-phase E. coli cells for primer binding sites located 6-7, 7-8, or 8-9 base pairs downstream of the promoter −10 element (mean ± SD, N = 3).

    Techniques Used: Sequencing, Binding Assay

    Promoter-sequence dependence of primer-dependent initiation: sequences flanking the primer binding site. Sequence logo ( 35 ) for primer-dependent initiation at TSS positions 7, 8, and 9 (corresponding to primer binding sites 6-7, 7-8, and 8-9, respectively) in stationary-phase E. coli cells (left) or in vitro , with the dinucleotide primer UpA (right). The height of each base “X” at each position “Y” represents the log 2 average of the % 5′-OH RNAs computed across sequences containing nontemplate-strand X at position Y. Red, consensus nucleotides; black, non-consensus nucleotides. Other symbols and colors as in Figure 1 .
    Figure Legend Snippet: Promoter-sequence dependence of primer-dependent initiation: sequences flanking the primer binding site. Sequence logo ( 35 ) for primer-dependent initiation at TSS positions 7, 8, and 9 (corresponding to primer binding sites 6-7, 7-8, and 8-9, respectively) in stationary-phase E. coli cells (left) or in vitro , with the dinucleotide primer UpA (right). The height of each base “X” at each position “Y” represents the log 2 average of the % 5′-OH RNAs computed across sequences containing nontemplate-strand X at position Y. Red, consensus nucleotides; black, non-consensus nucleotides. Other symbols and colors as in Figure 1 .

    Techniques Used: Sequencing, Binding Assay, In Vitro

    Promoter-sequence dependence of primer-dependent initiation: chromosomal promoters A. Sequence logo ( 35 ) for primer-dependent initiation at TSS positions 7, 8, and 9 (corresponding to primer binding sites 6-7, 7-8, and 8-9, respectively) in stationary-phase E. coli cells for 93 natural, chromosomally-encoded promoters that use UpA as a primer. The height of each base “X” at each position “Y” represents the log 2 average of the % 5′-OH RNAs computed across sequences containing nontemplate-strand X at position Y. Red, consensus nucleotides; black, non-consensus nucleotides. Other symbols and colors as in Figure 1 . B. Promoter-sequence dependence of primer-dependent initiation at the E. coli bhsA promoter. Top: sequences of DNA templates containing wild-type and mutant derivatives of bhsA promoter. Bottom: primer extension analysis of 5′-end lengths of bhsA RNAs. In primer-dependent initiation with a dinucleotide primer, the RNA product acquires one additional nucleotide at the RNA 5′ end ( Figure 1 ). Gel shows radiolabeled cDNA products derived from primer-independent initiation (5′-ppp) and primer-dependent initiation (5′-OH) in stationary-phase E. coli cells. Bottom right: ratios of primer-dependent initiation vs. primer-independent initiation (mean ± SD, N = 4).
    Figure Legend Snippet: Promoter-sequence dependence of primer-dependent initiation: chromosomal promoters A. Sequence logo ( 35 ) for primer-dependent initiation at TSS positions 7, 8, and 9 (corresponding to primer binding sites 6-7, 7-8, and 8-9, respectively) in stationary-phase E. coli cells for 93 natural, chromosomally-encoded promoters that use UpA as a primer. The height of each base “X” at each position “Y” represents the log 2 average of the % 5′-OH RNAs computed across sequences containing nontemplate-strand X at position Y. Red, consensus nucleotides; black, non-consensus nucleotides. Other symbols and colors as in Figure 1 . B. Promoter-sequence dependence of primer-dependent initiation at the E. coli bhsA promoter. Top: sequences of DNA templates containing wild-type and mutant derivatives of bhsA promoter. Bottom: primer extension analysis of 5′-end lengths of bhsA RNAs. In primer-dependent initiation with a dinucleotide primer, the RNA product acquires one additional nucleotide at the RNA 5′ end ( Figure 1 ). Gel shows radiolabeled cDNA products derived from primer-independent initiation (5′-ppp) and primer-dependent initiation (5′-OH) in stationary-phase E. coli cells. Bottom right: ratios of primer-dependent initiation vs. primer-independent initiation (mean ± SD, N = 4).

    Techniques Used: Sequencing, Binding Assay, Mutagenesis, Derivative Assay

    Related Articles

    Two-Dimensional Gel Electrophoresis:

    Article Title: A preclinical mouse model of glioma with an alternative mechanism of telomere maintenance (ALT)
    Article Snippet: Images were captured and analyzed using an Axioplan fluorescence microscope (Zeiss, Germany) with the appropriate filters and M-FISH software (ISIS, MetaSystems). .. 2D gel electrophoresis and genomic blotting DNA was phenol-chloroform extracted, ethanol precipitated, resuspended in nuclease-free water, and digested with MboI (New England Biolabs) for 4 hr at 37°C. ..

    Electrophoresis:

    Article Title: A preclinical mouse model of glioma with an alternative mechanism of telomere maintenance (ALT)
    Article Snippet: Images were captured and analyzed using an Axioplan fluorescence microscope (Zeiss, Germany) with the appropriate filters and M-FISH software (ISIS, MetaSystems). .. 2D gel electrophoresis and genomic blotting DNA was phenol-chloroform extracted, ethanol precipitated, resuspended in nuclease-free water, and digested with MboI (New England Biolabs) for 4 hr at 37°C. ..

    Article Title: Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli
    Article Snippet: For RNA products isolated from in vitro reactions, oligo i105 was used for RNAs processed by Rpp, oligo i106 was used for unprocessed RNAs (mock Rpp treated); oligo i107 was used for RNAs processed by PNK, and oligo i108 was used for unprocessed RNAs (mock PNK treated). .. Processed RNA products isolated from stationary-phase E. coli cells (in 10.5 μl of nuclease-free water) were combined with 1 mM ATP (NEB), 40 U RNaseOUT, 1x T4 RNA ligase buffer (NEB), and 10 U T4 RNA ligase 1 (NEB) and 1 μM of 5’ adaptor oligo (total reaction volume = 20 μl), and incubated at 37°C for 2 h. Reactions were then supplemented with 1x T4 RNA ligase buffer, 1 mM ATP, PEG 8000 (10% final), 5U T4 RNA ligase 1, and 20 U RNaseOUT (total reaction volume = 30 μl) and further incubated at 16°C for 16 h. Processed RNA products isolated from in vitro reactions (in 10.5 μl of nuclease-free water) were combined with PEG 8000 (10% final concentration), 1 mM ATP, 40 U RNaseOUT, 1x T4 RNA ligase buffer, 10 U T4 RNA ligase 1, and 1 μM of 5’ adaptor oligo (total reaction volume = 30 μl), and incubated at 16°C for 16 h. Ligation reactions were stopped by addition of 30 μl of 2x RNA loading dye and heated at 95°C for 5 min. For each replicate, the 4 ligation reactions were combined, and separated by electrophoresis on 10% 7M urea slab gels (equilibrated and run in 1x TBE). .. Gels were incubated with SYBR Gold nucleic acid gel stain, and bands were visualized with UV transillumination.

    other:

    Article Title: Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms in the 2014-15 influenza season
    Article Snippet: Once beads were completely dry, samples were eluted in 7.5μL of nuclease free water for five minutes prior to collection.

    Article Title: Detailed temporal dissection of an enhancer cluster reveals two distinct roles for individual elements
    Article Snippet: 1 μL of 5’ RNA adapter (50 μM) was diluted in 4 μL of RNase-free water and the RNA pellet was dissolved in this RNA-adapter dilution.

    Isolation:

    Article Title: Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli
    Article Snippet: For RNA products isolated from in vitro reactions, oligo i105 was used for RNAs processed by Rpp, oligo i106 was used for unprocessed RNAs (mock Rpp treated); oligo i107 was used for RNAs processed by PNK, and oligo i108 was used for unprocessed RNAs (mock PNK treated). .. Processed RNA products isolated from stationary-phase E. coli cells (in 10.5 μl of nuclease-free water) were combined with 1 mM ATP (NEB), 40 U RNaseOUT, 1x T4 RNA ligase buffer (NEB), and 10 U T4 RNA ligase 1 (NEB) and 1 μM of 5’ adaptor oligo (total reaction volume = 20 μl), and incubated at 37°C for 2 h. Reactions were then supplemented with 1x T4 RNA ligase buffer, 1 mM ATP, PEG 8000 (10% final), 5U T4 RNA ligase 1, and 20 U RNaseOUT (total reaction volume = 30 μl) and further incubated at 16°C for 16 h. Processed RNA products isolated from in vitro reactions (in 10.5 μl of nuclease-free water) were combined with PEG 8000 (10% final concentration), 1 mM ATP, 40 U RNaseOUT, 1x T4 RNA ligase buffer, 10 U T4 RNA ligase 1, and 1 μM of 5’ adaptor oligo (total reaction volume = 30 μl), and incubated at 16°C for 16 h. Ligation reactions were stopped by addition of 30 μl of 2x RNA loading dye and heated at 95°C for 5 min. For each replicate, the 4 ligation reactions were combined, and separated by electrophoresis on 10% 7M urea slab gels (equilibrated and run in 1x TBE). .. Gels were incubated with SYBR Gold nucleic acid gel stain, and bands were visualized with UV transillumination.

    Incubation:

    Article Title: Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli
    Article Snippet: For RNA products isolated from in vitro reactions, oligo i105 was used for RNAs processed by Rpp, oligo i106 was used for unprocessed RNAs (mock Rpp treated); oligo i107 was used for RNAs processed by PNK, and oligo i108 was used for unprocessed RNAs (mock PNK treated). .. Processed RNA products isolated from stationary-phase E. coli cells (in 10.5 μl of nuclease-free water) were combined with 1 mM ATP (NEB), 40 U RNaseOUT, 1x T4 RNA ligase buffer (NEB), and 10 U T4 RNA ligase 1 (NEB) and 1 μM of 5’ adaptor oligo (total reaction volume = 20 μl), and incubated at 37°C for 2 h. Reactions were then supplemented with 1x T4 RNA ligase buffer, 1 mM ATP, PEG 8000 (10% final), 5U T4 RNA ligase 1, and 20 U RNaseOUT (total reaction volume = 30 μl) and further incubated at 16°C for 16 h. Processed RNA products isolated from in vitro reactions (in 10.5 μl of nuclease-free water) were combined with PEG 8000 (10% final concentration), 1 mM ATP, 40 U RNaseOUT, 1x T4 RNA ligase buffer, 10 U T4 RNA ligase 1, and 1 μM of 5’ adaptor oligo (total reaction volume = 30 μl), and incubated at 16°C for 16 h. Ligation reactions were stopped by addition of 30 μl of 2x RNA loading dye and heated at 95°C for 5 min. For each replicate, the 4 ligation reactions were combined, and separated by electrophoresis on 10% 7M urea slab gels (equilibrated and run in 1x TBE). .. Gels were incubated with SYBR Gold nucleic acid gel stain, and bands were visualized with UV transillumination.

    Article Title: Exopolysaccharide production in Caulobacter crescentus: A resource allocation trade-off between protection and proliferation
    Article Snippet: .. When used as a template for Sanger sequencing, 10 μl of the fresh PCR product was mixed with 8.5 μL nuclease free water, 1.0 μl NEB Buffer 4, 0.1 μL ExoT (NEB, Ipswich, MA) and 0.25 μL rSAP (NEB, Ipswich, MA) incubated at 37°C for 30 min and at 80°C for 15 min, and stored at -20°C. ..

    In Vitro:

    Article Title: Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli
    Article Snippet: For RNA products isolated from in vitro reactions, oligo i105 was used for RNAs processed by Rpp, oligo i106 was used for unprocessed RNAs (mock Rpp treated); oligo i107 was used for RNAs processed by PNK, and oligo i108 was used for unprocessed RNAs (mock PNK treated). .. Processed RNA products isolated from stationary-phase E. coli cells (in 10.5 μl of nuclease-free water) were combined with 1 mM ATP (NEB), 40 U RNaseOUT, 1x T4 RNA ligase buffer (NEB), and 10 U T4 RNA ligase 1 (NEB) and 1 μM of 5’ adaptor oligo (total reaction volume = 20 μl), and incubated at 37°C for 2 h. Reactions were then supplemented with 1x T4 RNA ligase buffer, 1 mM ATP, PEG 8000 (10% final), 5U T4 RNA ligase 1, and 20 U RNaseOUT (total reaction volume = 30 μl) and further incubated at 16°C for 16 h. Processed RNA products isolated from in vitro reactions (in 10.5 μl of nuclease-free water) were combined with PEG 8000 (10% final concentration), 1 mM ATP, 40 U RNaseOUT, 1x T4 RNA ligase buffer, 10 U T4 RNA ligase 1, and 1 μM of 5’ adaptor oligo (total reaction volume = 30 μl), and incubated at 16°C for 16 h. Ligation reactions were stopped by addition of 30 μl of 2x RNA loading dye and heated at 95°C for 5 min. For each replicate, the 4 ligation reactions were combined, and separated by electrophoresis on 10% 7M urea slab gels (equilibrated and run in 1x TBE). .. Gels were incubated with SYBR Gold nucleic acid gel stain, and bands were visualized with UV transillumination.

    Concentration Assay:

    Article Title: Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli
    Article Snippet: For RNA products isolated from in vitro reactions, oligo i105 was used for RNAs processed by Rpp, oligo i106 was used for unprocessed RNAs (mock Rpp treated); oligo i107 was used for RNAs processed by PNK, and oligo i108 was used for unprocessed RNAs (mock PNK treated). .. Processed RNA products isolated from stationary-phase E. coli cells (in 10.5 μl of nuclease-free water) were combined with 1 mM ATP (NEB), 40 U RNaseOUT, 1x T4 RNA ligase buffer (NEB), and 10 U T4 RNA ligase 1 (NEB) and 1 μM of 5’ adaptor oligo (total reaction volume = 20 μl), and incubated at 37°C for 2 h. Reactions were then supplemented with 1x T4 RNA ligase buffer, 1 mM ATP, PEG 8000 (10% final), 5U T4 RNA ligase 1, and 20 U RNaseOUT (total reaction volume = 30 μl) and further incubated at 16°C for 16 h. Processed RNA products isolated from in vitro reactions (in 10.5 μl of nuclease-free water) were combined with PEG 8000 (10% final concentration), 1 mM ATP, 40 U RNaseOUT, 1x T4 RNA ligase buffer, 10 U T4 RNA ligase 1, and 1 μM of 5’ adaptor oligo (total reaction volume = 30 μl), and incubated at 16°C for 16 h. Ligation reactions were stopped by addition of 30 μl of 2x RNA loading dye and heated at 95°C for 5 min. For each replicate, the 4 ligation reactions were combined, and separated by electrophoresis on 10% 7M urea slab gels (equilibrated and run in 1x TBE). .. Gels were incubated with SYBR Gold nucleic acid gel stain, and bands were visualized with UV transillumination.

    Ligation:

    Article Title: Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli
    Article Snippet: For RNA products isolated from in vitro reactions, oligo i105 was used for RNAs processed by Rpp, oligo i106 was used for unprocessed RNAs (mock Rpp treated); oligo i107 was used for RNAs processed by PNK, and oligo i108 was used for unprocessed RNAs (mock PNK treated). .. Processed RNA products isolated from stationary-phase E. coli cells (in 10.5 μl of nuclease-free water) were combined with 1 mM ATP (NEB), 40 U RNaseOUT, 1x T4 RNA ligase buffer (NEB), and 10 U T4 RNA ligase 1 (NEB) and 1 μM of 5’ adaptor oligo (total reaction volume = 20 μl), and incubated at 37°C for 2 h. Reactions were then supplemented with 1x T4 RNA ligase buffer, 1 mM ATP, PEG 8000 (10% final), 5U T4 RNA ligase 1, and 20 U RNaseOUT (total reaction volume = 30 μl) and further incubated at 16°C for 16 h. Processed RNA products isolated from in vitro reactions (in 10.5 μl of nuclease-free water) were combined with PEG 8000 (10% final concentration), 1 mM ATP, 40 U RNaseOUT, 1x T4 RNA ligase buffer, 10 U T4 RNA ligase 1, and 1 μM of 5’ adaptor oligo (total reaction volume = 30 μl), and incubated at 16°C for 16 h. Ligation reactions were stopped by addition of 30 μl of 2x RNA loading dye and heated at 95°C for 5 min. For each replicate, the 4 ligation reactions were combined, and separated by electrophoresis on 10% 7M urea slab gels (equilibrated and run in 1x TBE). .. Gels were incubated with SYBR Gold nucleic acid gel stain, and bands were visualized with UV transillumination.

    Purification:

    Article Title: Comprehensive Mapping of Key Regulatory Networks that Drive Oncogene Expression
    Article Snippet: Reaction mixture was then incubated at 50 degrees for 1h, and then 4 degrees for Gibson assembly reaction. .. Assembled plasmids were purified by isopropanol precipitation with GlycoBlue Coprecipitant (Thermo Fisher) and resuspended in Nuclease-free water and transformed into NEB10beta (New England Biolabs) electrocompetent cells according to the manufacturer’s directions. .. Following recovery, a small dilution series were plated to assess transformation efficiency and the remainder was grown in liquid culture in LB medium overnight at 37°C, followed by maxiprep with PureLink® HiPure Plasmid Filter Maxiprep Kit (Thermo Fisher).

    Transformation Assay:

    Article Title: Comprehensive Mapping of Key Regulatory Networks that Drive Oncogene Expression
    Article Snippet: Reaction mixture was then incubated at 50 degrees for 1h, and then 4 degrees for Gibson assembly reaction. .. Assembled plasmids were purified by isopropanol precipitation with GlycoBlue Coprecipitant (Thermo Fisher) and resuspended in Nuclease-free water and transformed into NEB10beta (New England Biolabs) electrocompetent cells according to the manufacturer’s directions. .. Following recovery, a small dilution series were plated to assess transformation efficiency and the remainder was grown in liquid culture in LB medium overnight at 37°C, followed by maxiprep with PureLink® HiPure Plasmid Filter Maxiprep Kit (Thermo Fisher).

    Sequencing:

    Article Title: Exopolysaccharide production in Caulobacter crescentus: A resource allocation trade-off between protection and proliferation
    Article Snippet: .. When used as a template for Sanger sequencing, 10 μl of the fresh PCR product was mixed with 8.5 μL nuclease free water, 1.0 μl NEB Buffer 4, 0.1 μL ExoT (NEB, Ipswich, MA) and 0.25 μL rSAP (NEB, Ipswich, MA) incubated at 37°C for 30 min and at 80°C for 15 min, and stored at -20°C. ..

    Polymerase Chain Reaction:

    Article Title: Exopolysaccharide production in Caulobacter crescentus: A resource allocation trade-off between protection and proliferation
    Article Snippet: .. When used as a template for Sanger sequencing, 10 μl of the fresh PCR product was mixed with 8.5 μL nuclease free water, 1.0 μl NEB Buffer 4, 0.1 μL ExoT (NEB, Ipswich, MA) and 0.25 μL rSAP (NEB, Ipswich, MA) incubated at 37°C for 30 min and at 80°C for 15 min, and stored at -20°C. ..

    Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
    • stationary phase e coli cells  (New England Biolabs)
    99
    New England Biolabs stationary phase e coli cells
    Distributions of 5′-end sequences for RNAs generated in primer-independent initiation and primer-dependent initiation in vivo and in vitro . A. lac CONS-N10 library. Base pairs in the N10 region are numbered based on their position relative to the promoter −10 element. Colors as in Figure 1B . B-C. RNA 5′-end distribution histograms (mean ± SD, N = 3) for RNAs generated by primer-independent initiation (top) or primer-dependent initiation (bottom) in stationary-phase E. coli cells (panel B) or in vitro , with the dinucleotide primer UpA (panel C). Dashed line indicates the mean 5′-end position (mean ± SD, N = 3).
    Stationary Phase E Coli Cells, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/stationary phase e coli cells/product/New England Biolabs
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    stationary phase e coli cells - by Bioz Stars, 2021-05
    99/100 stars
    		  Buy from Supplier

    Image Search Results


    Distributions of 5′-end sequences for RNAs generated in primer-independent initiation and primer-dependent initiation in vivo and in vitro . A. lac CONS-N10 library. Base pairs in the N10 region are numbered based on their position relative to the promoter −10 element. Colors as in Figure 1B . B-C. RNA 5′-end distribution histograms (mean ± SD, N = 3) for RNAs generated by primer-independent initiation (top) or primer-dependent initiation (bottom) in stationary-phase E. coli cells (panel B) or in vitro , with the dinucleotide primer UpA (panel C). Dashed line indicates the mean 5′-end position (mean ± SD, N = 3).

    Journal: bioRxiv

    Article Title: Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli

    doi: 10.1101/2021.04.06.438613

    Figure Lengend Snippet: Distributions of 5′-end sequences for RNAs generated in primer-independent initiation and primer-dependent initiation in vivo and in vitro . A. lac CONS-N10 library. Base pairs in the N10 region are numbered based on their position relative to the promoter −10 element. Colors as in Figure 1B . B-C. RNA 5′-end distribution histograms (mean ± SD, N = 3) for RNAs generated by primer-independent initiation (top) or primer-dependent initiation (bottom) in stationary-phase E. coli cells (panel B) or in vitro , with the dinucleotide primer UpA (panel C). Dashed line indicates the mean 5′-end position (mean ± SD, N = 3).

    Article Snippet: Processed RNA products isolated from stationary-phase E. coli cells (in 10.5 μl of nuclease-free water) were combined with 1 mM ATP (NEB), 40 U RNaseOUT, 1x T4 RNA ligase buffer (NEB), and 10 U T4 RNA ligase 1 (NEB) and 1 μM of 5’ adaptor oligo (total reaction volume = 20 μl), and incubated at 37°C for 2 h. Reactions were then supplemented with 1x T4 RNA ligase buffer, 1 mM ATP, PEG 8000 (10% final), 5U T4 RNA ligase 1, and 20 U RNaseOUT (total reaction volume = 30 μl) and further incubated at 16°C for 16 h. Processed RNA products isolated from in vitro reactions (in 10.5 μl of nuclease-free water) were combined with PEG 8000 (10% final concentration), 1 mM ATP, 40 U RNaseOUT, 1x T4 RNA ligase buffer, 10 U T4 RNA ligase 1, and 1 μM of 5’ adaptor oligo (total reaction volume = 30 μl), and incubated at 16°C for 16 h. Ligation reactions were stopped by addition of 30 μl of 2x RNA loading dye and heated at 95°C for 5 min. For each replicate, the 4 ligation reactions were combined, and separated by electrophoresis on 10% 7M urea slab gels (equilibrated and run in 1x TBE).

    Techniques: Generated, In Vivo, In Vitro

    Promoter-sequence dependence of primer-dependent initiation in vivo : sequences flanking the primer binding site Sequence logo ( 35 ) for primer-dependent initiation in stationary-phase E. coli cells with each of the 16 dinucleotides at TSS positions 7, 8, and 9 (corresponding to primer binding sites 6-7, 7-8, and 8-9, respectively). The height of each base “X” at each position “Y” represents the log 2 average of the % 5′-OH RNAs computed across sequences containing nontemplate-strand X at position Y. Red, consensus nucleotides; black, non-consensus nucleotides. Gray box indicates positions where enrichment values could not be computed.

    Journal: bioRxiv

    Article Title: Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli

    doi: 10.1101/2021.04.06.438613

    Figure Lengend Snippet: Promoter-sequence dependence of primer-dependent initiation in vivo : sequences flanking the primer binding site Sequence logo ( 35 ) for primer-dependent initiation in stationary-phase E. coli cells with each of the 16 dinucleotides at TSS positions 7, 8, and 9 (corresponding to primer binding sites 6-7, 7-8, and 8-9, respectively). The height of each base “X” at each position “Y” represents the log 2 average of the % 5′-OH RNAs computed across sequences containing nontemplate-strand X at position Y. Red, consensus nucleotides; black, non-consensus nucleotides. Gray box indicates positions where enrichment values could not be computed.

    Article Snippet: Processed RNA products isolated from stationary-phase E. coli cells (in 10.5 μl of nuclease-free water) were combined with 1 mM ATP (NEB), 40 U RNaseOUT, 1x T4 RNA ligase buffer (NEB), and 10 U T4 RNA ligase 1 (NEB) and 1 μM of 5’ adaptor oligo (total reaction volume = 20 μl), and incubated at 37°C for 2 h. Reactions were then supplemented with 1x T4 RNA ligase buffer, 1 mM ATP, PEG 8000 (10% final), 5U T4 RNA ligase 1, and 20 U RNaseOUT (total reaction volume = 30 μl) and further incubated at 16°C for 16 h. Processed RNA products isolated from in vitro reactions (in 10.5 μl of nuclease-free water) were combined with PEG 8000 (10% final concentration), 1 mM ATP, 40 U RNaseOUT, 1x T4 RNA ligase buffer, 10 U T4 RNA ligase 1, and 1 μM of 5’ adaptor oligo (total reaction volume = 30 μl), and incubated at 16°C for 16 h. Ligation reactions were stopped by addition of 30 μl of 2x RNA loading dye and heated at 95°C for 5 min. For each replicate, the 4 ligation reactions were combined, and separated by electrophoresis on 10% 7M urea slab gels (equilibrated and run in 1x TBE).

    Techniques: Sequencing, In Vivo, Binding Assay

    Promoter-sequence dependence of primer-dependent initiation: primer binding site. A. Relative usage of dinucleotides in primer-dependent initiation in stationary-phase E. coli cells. Values represent the percentage of total 5′-OH RNAs generated using each of the 16 dinucleotide primers (mean, N = 3). Bold, dinucleotides preferentially used as primers. B. Complementarity between the primer binding site and dinucleotide in primer-dependent initiation. Top: primer-dependent initiation involving template-strand complementarity to both 5′ and 3′ nucleotides of primer (TSS-1, TSS), template-strand complementarity to only 3′ nucleotide of primer (TSS), template-strand complementarity to only 5′ nucleotide of primer (TSS-1), or no template-strand complementarity to primer (none). Three vertical lines, complementarity; X, non-complementarity. Other symbols and colors as in Figure 1 . Bottom: percentage of primer-dependent initiation involving complementarity to both 5′ and 3′ nucleotides of primer (TSS-1, TSS; pink), complementarity to only 3′ nucleotide of primer (TSS; purple), or template-strand complementarity to only 5′ nucleotide of primer or no template-strand complementarity to primer (TSS-1 or none; white) in stationary-phase E. coli cells (left) or in vitro , with the dinucleotide primer UpA (right) (mean ± SD, N = 3).

    Journal: bioRxiv

    Article Title: Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli

    doi: 10.1101/2021.04.06.438613

    Figure Lengend Snippet: Promoter-sequence dependence of primer-dependent initiation: primer binding site. A. Relative usage of dinucleotides in primer-dependent initiation in stationary-phase E. coli cells. Values represent the percentage of total 5′-OH RNAs generated using each of the 16 dinucleotide primers (mean, N = 3). Bold, dinucleotides preferentially used as primers. B. Complementarity between the primer binding site and dinucleotide in primer-dependent initiation. Top: primer-dependent initiation involving template-strand complementarity to both 5′ and 3′ nucleotides of primer (TSS-1, TSS), template-strand complementarity to only 3′ nucleotide of primer (TSS), template-strand complementarity to only 5′ nucleotide of primer (TSS-1), or no template-strand complementarity to primer (none). Three vertical lines, complementarity; X, non-complementarity. Other symbols and colors as in Figure 1 . Bottom: percentage of primer-dependent initiation involving complementarity to both 5′ and 3′ nucleotides of primer (TSS-1, TSS; pink), complementarity to only 3′ nucleotide of primer (TSS; purple), or template-strand complementarity to only 5′ nucleotide of primer or no template-strand complementarity to primer (TSS-1 or none; white) in stationary-phase E. coli cells (left) or in vitro , with the dinucleotide primer UpA (right) (mean ± SD, N = 3).

    Article Snippet: Processed RNA products isolated from stationary-phase E. coli cells (in 10.5 μl of nuclease-free water) were combined with 1 mM ATP (NEB), 40 U RNaseOUT, 1x T4 RNA ligase buffer (NEB), and 10 U T4 RNA ligase 1 (NEB) and 1 μM of 5’ adaptor oligo (total reaction volume = 20 μl), and incubated at 37°C for 2 h. Reactions were then supplemented with 1x T4 RNA ligase buffer, 1 mM ATP, PEG 8000 (10% final), 5U T4 RNA ligase 1, and 20 U RNaseOUT (total reaction volume = 30 μl) and further incubated at 16°C for 16 h. Processed RNA products isolated from in vitro reactions (in 10.5 μl of nuclease-free water) were combined with PEG 8000 (10% final concentration), 1 mM ATP, 40 U RNaseOUT, 1x T4 RNA ligase buffer, 10 U T4 RNA ligase 1, and 1 μM of 5’ adaptor oligo (total reaction volume = 30 μl), and incubated at 16°C for 16 h. Ligation reactions were stopped by addition of 30 μl of 2x RNA loading dye and heated at 95°C for 5 min. For each replicate, the 4 ligation reactions were combined, and separated by electrophoresis on 10% 7M urea slab gels (equilibrated and run in 1x TBE).

    Techniques: Sequencing, Binding Assay, Generated, In Vitro

    Promoter-sequence dependence of primer-dependent initiation in stationary-phase E. coli cells: primer binding site Top: primer-dependent initiation involving template-strand complementarity to both 5′ and 3′ nucleotides of primer (TSS-1, TSS), template-strand complementarity to only 3′ nucleotide of primer (TSS), template-strand complementarity to only 5′ nucleotide of primer (TSS-1), or no template-strand complementarity to primer (none). Three vertical lines, complementarity; X, non-complementarity. Other symbols and colors as in Figure 1 . Bottom: percentage of primer-dependent initiation involving complementarity to both 5′ and 3′ nucleotides of primer (TSS-1, TSS; pink), complementarity to only 3′ nucleotide of primer (TSS; purple), or template-strand complementarity to only 5′ nucleotide of primer or no template-strand complementarity to primer (TSS-1 or none; white) in stationary-phase E. coli cells for primer binding sites located 6-7, 7-8, or 8-9 base pairs downstream of the promoter −10 element (mean ± SD, N = 3).

    Journal: bioRxiv

    Article Title: Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli

    doi: 10.1101/2021.04.06.438613

    Figure Lengend Snippet: Promoter-sequence dependence of primer-dependent initiation in stationary-phase E. coli cells: primer binding site Top: primer-dependent initiation involving template-strand complementarity to both 5′ and 3′ nucleotides of primer (TSS-1, TSS), template-strand complementarity to only 3′ nucleotide of primer (TSS), template-strand complementarity to only 5′ nucleotide of primer (TSS-1), or no template-strand complementarity to primer (none). Three vertical lines, complementarity; X, non-complementarity. Other symbols and colors as in Figure 1 . Bottom: percentage of primer-dependent initiation involving complementarity to both 5′ and 3′ nucleotides of primer (TSS-1, TSS; pink), complementarity to only 3′ nucleotide of primer (TSS; purple), or template-strand complementarity to only 5′ nucleotide of primer or no template-strand complementarity to primer (TSS-1 or none; white) in stationary-phase E. coli cells for primer binding sites located 6-7, 7-8, or 8-9 base pairs downstream of the promoter −10 element (mean ± SD, N = 3).

    Article Snippet: Processed RNA products isolated from stationary-phase E. coli cells (in 10.5 μl of nuclease-free water) were combined with 1 mM ATP (NEB), 40 U RNaseOUT, 1x T4 RNA ligase buffer (NEB), and 10 U T4 RNA ligase 1 (NEB) and 1 μM of 5’ adaptor oligo (total reaction volume = 20 μl), and incubated at 37°C for 2 h. Reactions were then supplemented with 1x T4 RNA ligase buffer, 1 mM ATP, PEG 8000 (10% final), 5U T4 RNA ligase 1, and 20 U RNaseOUT (total reaction volume = 30 μl) and further incubated at 16°C for 16 h. Processed RNA products isolated from in vitro reactions (in 10.5 μl of nuclease-free water) were combined with PEG 8000 (10% final concentration), 1 mM ATP, 40 U RNaseOUT, 1x T4 RNA ligase buffer, 10 U T4 RNA ligase 1, and 1 μM of 5’ adaptor oligo (total reaction volume = 30 μl), and incubated at 16°C for 16 h. Ligation reactions were stopped by addition of 30 μl of 2x RNA loading dye and heated at 95°C for 5 min. For each replicate, the 4 ligation reactions were combined, and separated by electrophoresis on 10% 7M urea slab gels (equilibrated and run in 1x TBE).

    Techniques: Sequencing, Binding Assay

    Promoter-sequence dependence of primer-dependent initiation: sequences flanking the primer binding site. Sequence logo ( 35 ) for primer-dependent initiation at TSS positions 7, 8, and 9 (corresponding to primer binding sites 6-7, 7-8, and 8-9, respectively) in stationary-phase E. coli cells (left) or in vitro , with the dinucleotide primer UpA (right). The height of each base “X” at each position “Y” represents the log 2 average of the % 5′-OH RNAs computed across sequences containing nontemplate-strand X at position Y. Red, consensus nucleotides; black, non-consensus nucleotides. Other symbols and colors as in Figure 1 .

    Journal: bioRxiv

    Article Title: Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli

    doi: 10.1101/2021.04.06.438613

    Figure Lengend Snippet: Promoter-sequence dependence of primer-dependent initiation: sequences flanking the primer binding site. Sequence logo ( 35 ) for primer-dependent initiation at TSS positions 7, 8, and 9 (corresponding to primer binding sites 6-7, 7-8, and 8-9, respectively) in stationary-phase E. coli cells (left) or in vitro , with the dinucleotide primer UpA (right). The height of each base “X” at each position “Y” represents the log 2 average of the % 5′-OH RNAs computed across sequences containing nontemplate-strand X at position Y. Red, consensus nucleotides; black, non-consensus nucleotides. Other symbols and colors as in Figure 1 .

    Article Snippet: Processed RNA products isolated from stationary-phase E. coli cells (in 10.5 μl of nuclease-free water) were combined with 1 mM ATP (NEB), 40 U RNaseOUT, 1x T4 RNA ligase buffer (NEB), and 10 U T4 RNA ligase 1 (NEB) and 1 μM of 5’ adaptor oligo (total reaction volume = 20 μl), and incubated at 37°C for 2 h. Reactions were then supplemented with 1x T4 RNA ligase buffer, 1 mM ATP, PEG 8000 (10% final), 5U T4 RNA ligase 1, and 20 U RNaseOUT (total reaction volume = 30 μl) and further incubated at 16°C for 16 h. Processed RNA products isolated from in vitro reactions (in 10.5 μl of nuclease-free water) were combined with PEG 8000 (10% final concentration), 1 mM ATP, 40 U RNaseOUT, 1x T4 RNA ligase buffer, 10 U T4 RNA ligase 1, and 1 μM of 5’ adaptor oligo (total reaction volume = 30 μl), and incubated at 16°C for 16 h. Ligation reactions were stopped by addition of 30 μl of 2x RNA loading dye and heated at 95°C for 5 min. For each replicate, the 4 ligation reactions were combined, and separated by electrophoresis on 10% 7M urea slab gels (equilibrated and run in 1x TBE).

    Techniques: Sequencing, Binding Assay, In Vitro

    Promoter-sequence dependence of primer-dependent initiation: chromosomal promoters A. Sequence logo ( 35 ) for primer-dependent initiation at TSS positions 7, 8, and 9 (corresponding to primer binding sites 6-7, 7-8, and 8-9, respectively) in stationary-phase E. coli cells for 93 natural, chromosomally-encoded promoters that use UpA as a primer. The height of each base “X” at each position “Y” represents the log 2 average of the % 5′-OH RNAs computed across sequences containing nontemplate-strand X at position Y. Red, consensus nucleotides; black, non-consensus nucleotides. Other symbols and colors as in Figure 1 . B. Promoter-sequence dependence of primer-dependent initiation at the E. coli bhsA promoter. Top: sequences of DNA templates containing wild-type and mutant derivatives of bhsA promoter. Bottom: primer extension analysis of 5′-end lengths of bhsA RNAs. In primer-dependent initiation with a dinucleotide primer, the RNA product acquires one additional nucleotide at the RNA 5′ end ( Figure 1 ). Gel shows radiolabeled cDNA products derived from primer-independent initiation (5′-ppp) and primer-dependent initiation (5′-OH) in stationary-phase E. coli cells. Bottom right: ratios of primer-dependent initiation vs. primer-independent initiation (mean ± SD, N = 4).

    Journal: bioRxiv

    Article Title: Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli

    doi: 10.1101/2021.04.06.438613

    Figure Lengend Snippet: Promoter-sequence dependence of primer-dependent initiation: chromosomal promoters A. Sequence logo ( 35 ) for primer-dependent initiation at TSS positions 7, 8, and 9 (corresponding to primer binding sites 6-7, 7-8, and 8-9, respectively) in stationary-phase E. coli cells for 93 natural, chromosomally-encoded promoters that use UpA as a primer. The height of each base “X” at each position “Y” represents the log 2 average of the % 5′-OH RNAs computed across sequences containing nontemplate-strand X at position Y. Red, consensus nucleotides; black, non-consensus nucleotides. Other symbols and colors as in Figure 1 . B. Promoter-sequence dependence of primer-dependent initiation at the E. coli bhsA promoter. Top: sequences of DNA templates containing wild-type and mutant derivatives of bhsA promoter. Bottom: primer extension analysis of 5′-end lengths of bhsA RNAs. In primer-dependent initiation with a dinucleotide primer, the RNA product acquires one additional nucleotide at the RNA 5′ end ( Figure 1 ). Gel shows radiolabeled cDNA products derived from primer-independent initiation (5′-ppp) and primer-dependent initiation (5′-OH) in stationary-phase E. coli cells. Bottom right: ratios of primer-dependent initiation vs. primer-independent initiation (mean ± SD, N = 4).

    Article Snippet: Processed RNA products isolated from stationary-phase E. coli cells (in 10.5 μl of nuclease-free water) were combined with 1 mM ATP (NEB), 40 U RNaseOUT, 1x T4 RNA ligase buffer (NEB), and 10 U T4 RNA ligase 1 (NEB) and 1 μM of 5’ adaptor oligo (total reaction volume = 20 μl), and incubated at 37°C for 2 h. Reactions were then supplemented with 1x T4 RNA ligase buffer, 1 mM ATP, PEG 8000 (10% final), 5U T4 RNA ligase 1, and 20 U RNaseOUT (total reaction volume = 30 μl) and further incubated at 16°C for 16 h. Processed RNA products isolated from in vitro reactions (in 10.5 μl of nuclease-free water) were combined with PEG 8000 (10% final concentration), 1 mM ATP, 40 U RNaseOUT, 1x T4 RNA ligase buffer, 10 U T4 RNA ligase 1, and 1 μM of 5’ adaptor oligo (total reaction volume = 30 μl), and incubated at 16°C for 16 h. Ligation reactions were stopped by addition of 30 μl of 2x RNA loading dye and heated at 95°C for 5 min. For each replicate, the 4 ligation reactions were combined, and separated by electrophoresis on 10% 7M urea slab gels (equilibrated and run in 1x TBE).

    Techniques: Sequencing, Binding Assay, Mutagenesis, Derivative Assay