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Sample GSM1684594 Query DataSets for GSM1684594
Status Public on Sep 01, 2017
Title Nannochloropsis oceanica (IMET1, log phase)
Sample type SRA
 
Source name Nannochloropsis oceanica (IMET1, log phase)_Whole organism
Organism Nannochloropsis oceanica
Characteristics strain: IMET1
growth phase: log phase
Extracted molecule genomic DNA
Extraction protocol N. oceanica IMET1 was cultivated in f/2 liquid medium with 4mM NO3- under continuous light at 50 micromol photons m^(-2)s^(-1) until mid-log phase. Culture was pelleted and nucleic acid was extracted using phenol-chlorophorm and treated with RNase to degrade RNA.
5-10ug of gDNA was sheared to >10kb using g-tube (Covaris). The sheared DNA was treated with DNA damage repair mix followed by end repair and ligation of SMRT hairpin adapters using SMRTbell Template Preparation Reagent Kit (Pacific Biosciences). Fragments without adaptors are digested with exonuclease. Libraries were sequenced on Pacific Biosciences RSII sequencer using standard protocols.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model PacBio RS II
 
Data processing SMRT sequencing reads were processed and mapped to the respective reference genome sequences using the SMRTPortal Analysis platform, v.2.3.0 with BLASR mapping algorithm using the standard mapping protocol and the modifications protocol using default parameters.
Genome_build: N.oceanica_IMET1 (http://www.bioenergychina.org/fg/d.wang_genomes/)
The pipeline used to detect the modifications is called “DNA Modification Detection with SMRT Sequencing using R” and can be found at https://github.com/PacificBiosciences/kineticsTools. Interpulse durations (IPDs) were measured for all pulses aligned to each position in the reference sequence. The format of the output CSV/GFF files with modifications is described at http://www.pacb.com/pdf/TN_Detecting_DNA_Base_Modifications.pdf. The CSV file contains statistical analysis of each position in the reference. The GFF file includes sequence contexts only for sites of putative modification defined as positions with p-values of 0.01 or less.
Supplementary_files_format_and_content: GFF and CSV files
 
Submission date May 13, 2015
Last update date May 15, 2019
Contact name Denis Tolkunov
Organization name DOE Joint Genome Institute
Street address 2800 Mitchell Dr
City Walnut Creek
State/province CA
ZIP/Postal code 94598
Country USA
 
Platform ID GPL20198
Series (1)
GSE68860 Genome-wide single-molecule sequencing of 6-methyladenine in eukaryotes
Relations
BioSample SAMN03657261
SRA SRX1026808

Supplementary file Size Download File type/resource
GSM1684594_Nanno.modifications.csv.gz 767.5 Mb (ftp)(http) CSV
GSM1684594_Nanno.modifications.gff.gz 20.0 Mb (ftp)(http) GFF
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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