|
Status |
Public on Jun 25, 2020 |
Title |
S2-DSRC genomic DNA control |
Sample type |
SRA |
|
|
Source name |
S2-DSRC cells
|
Organism |
Drosophila melanogaster |
Characteristics |
cell line: S2-DSRC cells m6a-mtase conditions: N/A
|
Treatment protocol |
Nuclei were extracted using 0.05% IGEPAL in Buffer A (50 mM Tris-HCl, pH 8; 100mM NaCl; 1mM DTT) for 10 minutes at 4 degrees. Nuclei were treated with m6A-Mtase as above and genomic DNA was extracted then subjected to shearing and then PacBio library construction.
|
Growth protocol |
S2-DSRC cells were grown at room temerature to 90% confluency. K562 cells were grown at 37C to 5x10^5 cells/mL.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
PCR-free PacBio libraries were constructed using standard protocol. Long-read PacBio HiFi/CCS sequencing
|
|
|
Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Sequel |
|
|
Description |
DS76914
|
Data processing |
Library strategy: DNA-seq Pacbio software pbalign, bamSieve, ipdSummary from smrtlink-release_8.0.0.79519 Subreads were aligned using pbalign --concordant --hitPolicy=randombest --minAccuracy 70 --minLength 50 bamSieve was used to extract single-molecule-coverage subsets of the aligned data for analysis with ipdSummary --pvalue 0.001 --identify m6A Genome_build: dm6 Supplementary_files_format_and_content: bed formatted mapped molecule locations with ZMW ID in column 4
|
|
|
Submission date |
Mar 13, 2020 |
Last update date |
Jun 25, 2020 |
Contact name |
John A Stamatoyannopoulos |
E-mail(s) |
jstam@altius.org
|
Organization name |
Altius Institute / University of Washington
|
Department |
Genome Sciences
|
Lab |
Stamatoyannopoulos
|
Street address |
2211 Elliott Avenue, 6th Floor
|
City |
SEATTLE |
State/province |
WA |
ZIP/Postal code |
98121 |
Country |
USA |
|
|
Platform ID |
GPL28354 |
Series (2) |
GSE146940 |
Single-molecule regulatory architectures captured by chromatin fiber sequencing [Dm Fiber-seq] |
GSE146942 |
Single-molecule regulatory architectures captured by chromatin fiber sequencing |
|
Relations |
BioSample |
SAMN14374578 |
SRA |
SRX7909063 |