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Strain MK423 was grown under the same conditions as used when growing cells for microscopy analysis; cells of OD600 = 0.4 were diluted 100-fold in C+Y medium with 0.1 mM ZnCl2 and incubated for 2.5 hours until OD600 = 0.15. Cells were then harvested by centrifugation for 5 min at 6500 x g at 4°C. Genomic DNA was isolated using the Wizard® Genomic DNA Purification Kit (Promega) as described previously (Slager et al. 2014 Cell). Fragmentation was performed using Covaris instrument, and libraries
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Strain MK422 was grown under the same conditions as used when growing cells for microscopy analysis; cells of OD600 = 0.4 were diluted 100-fold in C+Y medium with 0.1 mM ZnCl2 and incubated for 2.5 hours until OD600 = 0.15. Cells were then harvested by centrifugation for 5 min at 6500 x g at 4°C. Genomic DNA was isolated using the Wizard® Genomic DNA Purification Kit (Promega) as described previously (Slager et al. 2014 Cell). Fragmentation was performed using Covaris instrument, and libraries
...

Strain MK350 was grown under the same conditions as used when growing cells for microscopy analysis; cells of OD600 = 0.4 were diluted 100-fold in C+Y medium with 0.1 mM ZnCl2 and incubated for 2.5 hours until OD600 = 0.15. Cells were then harvested by centrifugation for 5 min at 6500 x g at 4°C. Genomic DNA was isolated using the Wizard® Genomic DNA Purification Kit (Promega) as described previously (Slager et al. 2014 Cell). Fragmentation was performed using Covaris instrument, and libraries
...

WT 110901_SN865_B_L006_R1_GQC-28-
ATCACG.fastq.gz
100 19.624.852 1,29

llumina fastq format
4 lines for each sequence:
1- Unique identifier, with the following format:
@::::#/
2- Sequence (A, T, C ,G or N (undetermined) only)
3- Orientation (always forward without mapping)
4- Quality value for each base, corresponding to a Phred-like score encoded in ASCII format, with an
offset of of 33 (e.g. “J” gives a value of 41) and is in accordance with sanger FASTQ format.
The sequence file is compressed
...

S. pneumoniae RNA-Seq
Barcodes:
HPUra 1: CAGATC
HPUra 2: ACTTGA
Kanamycin: AGTCAA

S. pneumoniae RNA-Seq
Barcodes:
Control 1: CAGATC
Control 2: ACTTGA

E. coli RNA-Seq
Barcodes:
Trimethoprim 1: CCGTCC
Trimethoprim 2: GTAGAG

E. coli RNA-Seq
Barcodes:
Control 1: AGTTCC
Control 2: ATGTCA

E. coli DNA-Seq
Barcodes:
control 1: GTGGCC
control 2: GTTTCG
Trimethoprim 1: CACTCA
Trimethoprim 2: CAGGCG

S. pneumoniae kanamycin DNA PE2

S. pneumoniae kanamycin DNA PE1

S. pneumoniae HPUra 2 DNA PE2

S. pneumoniae HPUra 2 DNA PE1

S. pneumoniae HPUra 1 DNA PE2

S. pneumoniae HPUra 1 DNA PE1

S. pneumoniae Control 2 DNA PE2

S. pneumoniae Control 2 DNA PE1

S. pneumoniae Control 1 DNA PE2

S. pneumoniae Control1 DNA-Seq PE1

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