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Sample GSM5770596

Query DataSets for GSM5770596

Status

Public on Jan 05, 2022

Title

M9 Min Glu #2, Input, replicate 2

Sample type

SRA

Source name

Culture lysate

Organism

Escherichia coli

Characteristics

strain: K12 MG1655
genotype: wild type
media: M9 minimal media + glucose
time of harvest: logarithmic phase (after growth in KDG)

Treatment protocol

Upon the harvest points noted under ‘growth protocol’, 1 mL of sample was preserved in Qiagen RNAprotect bacterial reagent following the manufacturer’s instructions

Growth protocol

Overnight cultures (in M9 minimal media + 0.02% glucose) were back diluted to an OD600 0.003 in fresh, prewarmed M9 minimal medium including 0.2% glucose at 37°C. After growth to an OD of 0.2, the Glu #1 sample was harvested. Remaining cells were diluted to an OD of ~0.1 in M9 ninimal medium including 0.2% 5-keto D-gluconic acid, and grown to an OD of 0.2, at which point the KDG sample was harvested. Remaining cells were diluted in M9 minimal media plus 0.2% glucose to an OD of 0.003, and grown to an OD of 0.2, at which point the Glu #2 sample was harvested.

Extracted molecule

genomic DNA

Extraction protocol

DNA samples: Frozen cell pellets were resuspended in 1x IPOD lysis buffer (10 mM Tris HCl, pH 8.0; 50 mM NaCl) containing 1x protease inhibitors (Roche Complete Mini, EDTA free) and 52.5 kU/mL of ready-lyse (Epicentre); 600 uL per pellet (stationary phase cells were diluted 10x prior to lysis due to the much higher biomass of those pellets). We incubated the resuspended pellet for 15 minutes at 30 C, and then placed it on ice. We then sonicated the cells using a Branson digital sonicator at 25% power, using three 10 second bursts with 10 second pauses between bursts. The cells were maintained in a wet ice bath throughout sonication. We then performed a calibrated DNA digestion to sub-200 bp fragments, by adding to the sonicated lysates 60 ug RNase A (Thermo Fisher), 6 uL DNase I (Fisher product #89835), 5.4 uL 100 mM MnCl2, and 4.5 uL 100 mM CaCl2, and then incubating on ice. While the appropriate digestion time must be calibrated for each particular sample type and batch of DNase, 30 minutes of digestion proved appropriate for all samples here. Reactions were quenched after completion by the addition of 50 uL 500 mM EDTA (pH 8.0), typically yielding 50-200 bp fragments. Samples were clarified by centrifugation for 10 minutes at 16,9000xg at 4 C. After clarification, the lysate was mixed with 1 volume of 100 mM Tris base and 2 volumes of 25:24:1 phenol:chloroform:isoamyl alcohol, vortexed, and then incubated for 10 minutes at room temperature. After incubation, the sample was spun at 21,130xg for two minutes at room temperature, allowing formation of a white disc at the aqueous-organic interface enriched for protein-DNA complexes. The complete aqueous phases were removed and discarded, and the remaining disc washed again with 350 microliters TE (10 mM Tris, pH 8.0; 1 mM EDTA), 350 microliters 100 mM Tris base, and 700 microliters 24:1 chloroform:isoamyl alcohol. The resulting mixture was vortexed vigorously, and again centrifuged for 2 minutes at 21,130xg. All liquid was again removed, and the wash was repeated using 700 microliters TE and 700 microliters 24:1 chloroform:isoamyl alcohol. After vortexing, centrifugation, and removal of the final wash (exactly as above), any residual liquid was removed by wicking with a laboratory wipe (if any substantial pools of liquid were present). Finally, the interface was resuspended in 500 microliters of elution buffer (described above), vortexed vigorously, and reverse crosslinked overnight at 65 C. After allowing the samples to cool to room temperature, we then added 100ug of RNase A (Thermo-Fisher), incubated 2 hours at 37 C, then added 200ug of proteinase K (Fermentas) and incubated an additional 2 hours at 50 C. DNA was then recovered via standard phenol-chloroform extraction and ethanol precipitation, following protocols from (Ausubel, 1998). We used Glycoblue (Ambion) as a co-precipitant, NaCl as a precipitating salt (due to the presence of SDS in our solution), and washed with ice-cold 95% ethanol to avoid loss of low molecular weight DNA. RNA: RNA was harvested using Qiagen RNAProtect. RNA was isolated, and rRNA depletion was performed according to the Illumina Ribo-Zero rRNA Removal Kit for Bacteria.
DNA samples: NEB Nebnext Ultra 2 DNA kit, but with a spin column replacing the first bead cleanup (see the accompanying paper for details).

Library strategy

ChIP-Seq

Library source

genomic

Library selection

ChIP

Instrument model

Illumina NovaSeq 6000

Description

wt_minglu2_chip_vs_inp_lograt.gr
wt_minglu2_chip_vs_inp_lograt.bed
wt_minglu2_v6rz_chipsub.gr
wt_minglu2_v6rz_chipsub.bed

Data processing

Adapter removal using the common Illumina Truseq adapter sequences with cutadapt 1.8.1
Read ends were trimmed using Trimmomatic 0.33 in paired end mode, with the trimming steps ‘TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:10’
Reads were aligned using bowtie2 version 2.1.0 with ‘very sensitive’ end-to-end presets, and dovetailed alignments allowed
We performed gene-level quantitation with htseq-count, using union mode for scoring and all mode for non-unique assignments
Differential expression calling was then performed using deseq2 with default settings
Genome_build: U00096.3
Supplementary_files_format_and_content: .gr files: Occupancies (expressed as log2(chip/input) for ChIP samples, and robust z-scores (as defined in https://doi.org/10.1101/2020.01.29.924811) for IPOD samples. The first column gives a location and the second column gives the corresponding value
Supplementary_files_format_and_content: .csv files for RNA: Tabular output from DeSeq2, using as a sign convention log(cond2/cond1), where cond1 is the first condition listed and log2 the second condition listed in the file name
Supplementary_files_format_and_content: .bed files: Occupancies (expressed as log2(chip/input) for ChIP samples, and robust z-scores (as defined in https://doi.org/10.1101/2020.01.29.924811) for IPOD samples. Standard bed-formatted files

Submission date

Jan 04, 2022

Last update date

Jan 05, 2022

Contact name

Lydia Freddolino

E-mail(s)

[email protected]

Organization name

University of Michigan

Department

Biological Chemistry