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| Status |
Public on Sep 01, 2017 |
| Title |
Drosophila melanogaster |
| Sample type |
SRA |
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| Source name |
Drosophila melanogaster_Whole organism
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| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Whole organism
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Ref: Kim, K. E. et al. Scientific Data 1, 140045 (2014), doi:10.1038/sdata.2014.45
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
PacBio RS II |
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| Description |
[Third-party re-analysis] Raw SMRT sequencing data was retrieved from: http://datasets.pacb.com.s3.amazonaws.com/2014/Drosophila/reads/list.html. Ref: Kim, K. E. et al. Scientific Data 1, 140045 (2014), doi:10.1038/sdata.2014.45
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| 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: FlyBase dm6
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
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| Submission date |
May 13, 2015 |
| Last update date |
Sep 01, 2017 |
| Contact name |
Denis Tolkunov |
| Organization name |
DOE Joint Genome Institute
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| Street address |
2800 Mitchell Dr
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| City |
Walnut Creek |
| State/province |
CA |
| ZIP/Postal code |
94598 |
| Country |
USA |
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| Platform ID |
GPL20199 |
| Series (1) |
| GSE68860 |
Genome-wide single-molecule sequencing of 6-methyladenine in eukaryotes |
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| Relations |
| BioSample |
SAMN03657262 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1684595_Drosophila.modifications.csv.gz |
3.6 Gb |
(ftp)(http) |
CSV |
| GSM1684595_Drosophila.modifications.gff.gz |
97.5 Mb |
(ftp)(http) |
GFF |
| Processed data provided as supplementary file |
| Raw data not provided for this record |
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