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| Status |
Public on Jan 20, 2016 |
| Title |
Salmonella_enterica_enterica_sv_Paratyphi_B_SPB7_native |
| Sample type |
SRA |
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| Source name |
Bacterial gDNA
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| Organism |
Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB7 |
| Characteristics |
strain: SPB7
dna treatment: none
pacbio sequencing chemistry: C2 / C2
genome build (img genome id): 641228506
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
gDNA was randomly sheared, end repaired, and ligated to blunt end hairpin adapters to form standard SMRTbell templates
SMRT-sequencing
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
PacBio RS II |
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| Data processing |
Sequencing reads were processed and mapped to the respective reference sequences using the BLASR mapper (http://www.pacbiodevnet.com/SMRT-Analysis/Algorithms/BLASR) and the Pacific Biosciences' SMRT Analysis pipeline (http://www.pacbiodevnet.com/SMRT-Analysis/Software/SMRT-Pipe) using the standard mapping protocol.
To identify modified positions, we used Pacific Biosciences' SMRTPortal analysis platform, v. 2.0.1, which uses an in silico kinetic reference, and a t-test based kinetic score detection of modified base positions (details are available at http://www.pacb.com/pdf/TN_Detecting_DNA_Base_Modifications.pdf)
Modified sites were grouped into motifs using MotifFinder (v1)2.
Genome_build: As indicated by IMG genome ID in the individual samples section (http://img.jgi.doe.gov/home.html)
Supplementary_files_format_and_content: modifications.gff files are comma separated text files that contain data for genome positions with Qmod scores greater than 20; Data includes Qmod scores, IPD ratios, coverage, and sequence contexts for a +/- 20 nt window surrounding the modified position (see https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Methylome-Analysis-Technical-Note for more details)
Supplementary_files_format_and_content: modifications.csv files are comma separated text files that contain data for all positions (both strands) in the reference sequence; data includes Qmod score, IPD ratio, and coverage. (see https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Methylome-Analysis-Technical-Note for more details)
Supplementary_files_format_and_content: motif_summary.csv files contain the genome-wide summary of the methyltransferase recognition motifs discovered in this sample. (see https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Methylome-Analysis-Technical-Note for more details).
Supplementary_files_format_and_content: motifs.gff files are similar to the modifications.gff files. These files contain information about all sites detected as modified, all locations of a discovered motif (including those which are apparently unmodified), and also the overlap between the modifications and motifs. (see https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Methylome-Analysis-Technical-Note for more details).
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| Submission date |
Jun 15, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Matthew James Blow |
| E-mail(s) |
mjblow@lbl.gov
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| Phone |
510-486-6590
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| Fax |
510-486-7004
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| Organization name |
Lawrence Berkeley National Laboratory
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| Department |
Genomics Division
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| Lab |
Rubin / Pennacchio
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| Street address |
1 Cyclotron Road
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| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
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| Platform ID |
GPL20508 |
| Series (1) |
| GSE69872 |
The Epigenomic Landscape of Prokaryotes |
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| Relations |
| BioSample |
SAMN03775413 |
| SRA |
SRX1059003 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1711743_Salmonella_enterica_enterica_sv_Paratyphi_B_SPB7_native.modifications.csv.gz |
139.8 Mb |
(ftp)(http) |
CSV |
| GSM1711743_Salmonella_enterica_enterica_sv_Paratyphi_B_SPB7_native.modifications.gff.gz |
2.5 Mb |
(ftp)(http) |
GFF |
| GSM1711743_Salmonella_enterica_enterica_sv_Paratyphi_B_SPB7_native.motif_summary.csv.gz |
552 b |
(ftp)(http) |
CSV |
| GSM1711743_Salmonella_enterica_enterica_sv_Paratyphi_B_SPB7_native.motifs.gff.gz |
2.7 Mb |
(ftp)(http) |
GFF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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