|
| Status |
Public on May 05, 2015 |
| Title |
SMRT-sequencing |
| Sample type |
SRA |
| |
|
| Source name |
whole worm WT gDNA
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
developmental stage: WT (N2) mixed stage worms
|
| Treatment protocol |
Worms were fed dam-dcm- bacteria
|
| Growth protocol |
Mixed stage WT (N2) worms were grown at 20 degrees
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Worms were washed several times with M9 buffer and snap frozen in liquid nitrogen. Pellets were sent to Umass Medical School Deep Sequencing Core for gDNA extraction and SMRT sequencing
Library was constructed by Umass Medical School Deep sequencing core. Single Molecule Real Time Sequencing
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
PacBio RS II |
| |
|
| Data processing |
mapping using pbalign
The polymerase kinetics information was further loaded after alignment by loadChemistry.py and loadPulses scripts
post-aligned datasets were merged and sorted by using cmph5tools
m6A was identified using ipdSummary.py
Genome_build: ce10
m6A.gff
column: description
chr: chrromosome name
source: Name of tool -- "kinModCall"
type: Modification type -- a generic tag "modified_base" is used for unidentified bases. For identified bases, m6A, m4C, and m5C are used
start: start
end: end
score: -10 log (p-value) score for the detection of this event. Analogous to a Phred quality score. A value of 20 is the minimum default threshold for this file, and corresponds to a p-value of 0.01. A score of 30 corresponds to a pvalue of 0.001.
strand: Native sample strand where kinetics were generated. "+" is the strand of the original FASTA and "-" is the reverse complement of the strand. Note that in the .csv file these are marked "0" and "1" respectively.
phase: Not applicable
attibutes: Contains extra fields. IPDRatio is traditional IPD Ratio, context is the reference sequence -20bp to +20bp around the modification plus the base at this location as the 21st character, and sequencing coverage of that position. Context is always written in 5" -> 3" orientation of the template strand.
|
| |
|
| Submission date |
Mar 19, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Lei Gu |
| E-mail(s) |
lei.gu@mpi-bn.mpg.de
|
| Organization name |
Max Planck Institute for heart and lung research
|
| Street address |
parkstreet 1
|
| City |
Bad Nauheim |
| State/province |
MASSACHUSETTS |
| ZIP/Postal code |
61231 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19919 |
| Series (1) |
| GSE66504 |
Identification of N6-adenine methylation in C. elegans DNA |
|
| Relations |
| BioSample |
SAMN03435831 |
| SRA |
SRX961222 |
