|
| Status |
Public on Sep 01, 2018 |
| Title |
whole L4 stage wildtype C. elegans gDNA |
| Sample type |
SRA |
| |
|
| Source name |
whole L4 stage wildtype C. elegans gDNA
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
developmental stage: L4
|
| Growth protocol |
worms were grown on standard NGM plates with Ampicillin antibiotics and fed dam-dcm- bacteria
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
gDNA was extracted as per the protocol of Invitrogens PureLink Genomic DNA kit with 6 freeze thaws in liquid nitrogen before the isolation began
Library was constructed and sequenced at Umass Medical School Deep Sequencing core
SMRT-seq
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
PacBio RS II |
| |
|
| Data processing |
Base modification was detected using SMRT Analysis 2.3.0
The RS_Modification_Detection_and Motif_Analysis.1 protocal was used, only the unambiguously mapped reads with minimum map QV30 were used and reads in the modification detection step
The SMRT-seq data in the study GSE66504 was included to get enough coverage for detecting the modification.
Genome_build: ce10
Supplementary_files_format_and_content: GFF file is the output from the SMRT Analysis pipeline, it contains 4mCs sites information, coverage, IPD ratio, context sequence.
|
| |
|
| Submission date |
Sep 16, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jie Wang |
| E-mail(s) |
Jie.Wang@Roswellpark.org
|
| Organization name |
Roswell Park Comprehensive Cancer Center
|
| Department |
Department of Biostatistics and Bioinformatics
|
| Street address |
Elm and Carlton Streets
|
| City |
Buffalo |
| State/province |
NY |
| ZIP/Postal code |
14263 |
| Country |
USA |
| |
|
| Platform ID |
GPL19919 |
| Series (1) |
| GSE86993 |
DNA is Methylated on N4-Cytosine in Eukaryotes |
|
| Relations |
| BioSample |
SAMN05781271 |
| SRA |
SRX2170085 |
