NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4411221 Query DataSets for GSM4411221
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

Supplementary file Size Download File type/resource
GSM4411221_DS75527_ZMW_IDs_dm6.bed.gz 4.6 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap