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Sample GSM4411210 Query DataSets for GSM4411210
Status Public on Jun 25, 2020
Title S2-DSRC AdMTase-seq (2 U EcoGII)
Sample type SRA
 
Source name S2-DSRC cells
Organism Drosophila melanogaster
Characteristics cell line: S2-DSRC cells
m6a-mtase conditions: 2 U EcoGII for 20min at 37C
antibody: Millipore Sigma ABE572
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.
Growth protocol S2-DSRC cells were grown at room temerature to 90% confluency. K562 cells were grown at 37C to 5x10^5 cells/mL; Hela cells were grown at room temerature to 90% confluency
Extracted molecule genomic DNA
Extraction protocol Short DNA fragments were subjected to standard Illumina library construction
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 4000
 
Description DS69058
Data processing Library strategy: AdMTase-seq
Basecalling, RTA v1.13
Alignments to GRCh38, BWA v0.7.12
Read processing, Samtools v1.2
Read density, Bedops v2.4.15
Peak calling, Hotspot2 v2.1.1
Genome_build: dm6
Supplementary_files_format_and_content: 5% FDR peak calls as .bed file
 
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 GPL21306
Series (2)
GSE146937 Single-molecule regulatory architectures captured by chromatin fiber sequencing [Dm AdMTase-seq]
GSE146942 Single-molecule regulatory architectures captured by chromatin fiber sequencing
Relations
BioSample SAMN14374559
SRA SRX7909052

Supplementary file Size Download File type/resource
GSM4411210_DS69058_peaks_fdr05.bed.gz 126.5 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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