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Sample GSM4411222 Query DataSets for GSM4411222
Status Public on Jun 25, 2020
Title K562 Fiber-seq (500 U Hia5) rep1 run1
Sample type SRA
 
Source name K562 cells
Organism Homo sapiens
Characteristics cell line: K562
m6a-mtase conditions: 500 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 II
 
Description DS76915
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: hg38
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 GPL28352
Series (2)
GSE146941 Single-molecule regulatory architectures captured by chromatin fiber sequencing [Hs Fiber-seq]
GSE146942 Single-molecule regulatory architectures captured by chromatin fiber sequencing
Relations
BioSample SAMN14374586
SRA SRX7909608

Supplementary file Size Download File type/resource
GSM4411222_DS76915-run1_ZMW_IDs_hg38.bed.gz 36.3 Mb (ftp)(http) BED
GSM4411222_tracks_m6A_DS76915-run1.hg38.bed.gz 348.0 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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