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Sample GSM1711788 Query DataSets for GSM1711788
Status Public on Jan 20, 2016
Title Tolumonas_sp_BRL6_1_native
Sample type SRA
 
Source name Bacterial gDNA
Organism Tolumonas lignilytica
Characteristics strain: BRL6-1
dna treatment: none
pacbio sequencing chemistry: C2 / C2
genome build (img genome id): 2522125098
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
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model PacBio RS II
 
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).
 
Submission date Jun 15, 2015
Last update date May 15, 2019
Contact name Matthew James Blow
E-mail(s) mjblow@lbl.gov
Phone 510-486-6590
Fax 510-486-7004
Organization name Lawrence Berkeley National Laboratory
Department Genomics Division
Lab Rubin / Pennacchio
Street address 1 Cyclotron Road
City Berkeley
State/province CA
ZIP/Postal code 94720
Country USA
 
Platform ID GPL20553
Series (1)
GSE69872 The Epigenomic Landscape of Prokaryotes
Relations
BioSample SAMN03775517
SRA SRX1059048

Supplementary file Size Download File type/resource
GSM1711788_Tolumonas_sp_BRL6_1_native.modifications.csv.gz 103.9 Mb (ftp)(http) CSV
GSM1711788_Tolumonas_sp_BRL6_1_native.modifications.gff.gz 2.8 Mb (ftp)(http) GFF
GSM1711788_Tolumonas_sp_BRL6_1_native.motif_summary.csv.gz 408 b (ftp)(http) CSV
GSM1711788_Tolumonas_sp_BRL6_1_native.motifs.gff.gz 2.9 Mb (ftp)(http) GFF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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