|
| Status |
Public on Jun 25, 2020 |
| Title |
S2-DSRC Fiber-seq (20 U Hia5) |
| Sample type |
SRA |
| |
|
| Source name |
S2-DSRC cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: S2-DSRC cells
m6a-mtase conditions: 20 U Hia5 for 10min at 37C
|
| 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 |
DS76913
|
| 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 |
SAMN14374580 |
| SRA |
SRX7909061 |
