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Sample GSM5242407 Query DataSets for GSM5242407
Status Public on Sep 07, 2021
Title WT_H3K4me3_frozen_rep2
Sample type SRA
 
Source name Spleen
Organism Mus musculus
Characteristics strain: C57BL/6
genotype: wildtype
cell type: splenic B cells
cell state: frozen
target: H3K4me3
Extracted molecule genomic DNA
Extraction protocol Spleens were harvested from C57BL/6 mice and B cells were isolataed by MACS. Cells were used immediated for CUT&RUN (fresh) or cell pellets were resuspended in 90%FBS/10% DMSO and frozen overnight.
Libraries were prepared using the NEBnext Ultra II DNA Library Prep Kit (Illumina)
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 1500
 
Data processing Library strategy: CUT&RUN
File processing was carried out using CUT&RUNTools (Zhu et al., 2019)
Trimmomatic-0.36 was used to trim TruSeq adapters
Bowtie 2 2.2.9 was used with "--dovetail" option indicated
Picard 2.8.0 MarkDuplicates was used to mark PCR duplicates
MACS2 was used to callpeaks with options " -f BAMPE -q 0.01 -B --SPMR" indicated
Genome_build: mm10
Supplementary_files_format_and_content: peak files
 
Submission date Apr 15, 2021
Last update date Sep 07, 2021
Contact name Michaela Reagan
E-mail(s) michaela.reagan@mainehealth.org
Organization name MaineHealth Institute for Research
Department Center for Molecular Medicine
Street address 81 Research Drive
City Scarborough
State/province Maine
ZIP/Postal code 04074
Country USA
 
Platform ID GPL18480
Series (1)
GSE172130 An integrated CUT&RUN quality control workflow for histone modifications and transcription factors
Relations
BioSample SAMN18747091
SRA SRX10605816

Supplementary file Size Download File type/resource
GSM5242407_WT_H3K4me3_frozen_rep2.narrowPeak.gz 665.6 Kb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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