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Sample GSM5452705 Query DataSets for GSM5452705
Status Public on Jul 14, 2021
Title CUT&RUN IgG negative control TSA-500K K562 cells
Sample type SRA
Source name K562 cells
Organism Homo sapiens
Characteristics cell type: K562 human immortalised myelogenous leukemia cell line
treatment: 1 uM Trichostatin A (TSA) in wash buffer
antibody: CUTANA™ Rabbit IgG CUT&RUN Negative Control Antibody EpiCypher 13-0042, lot 20036001-52
Treatment protocol Native cells unless otherwise specified. For H3K18ac sample, 500K cells were crosslinked with 0.1% formaldehyde for 1 minute at room temperature, and then quenched with 125 mM glycine. For TSA experiments, native cells were harvested and during CUT&RUN all buffers were supplemented with 1uM TSA to prevent acetyl degradation.
Growth protocol K562 cells were maintained (1–10 × 10^5 cell/ml) in T25 flasks in IMDM + 10% FBS + 1% Pen/Strep
Extracted molecule genomic DNA
Extraction protocol CUTANA protocol v1.5.1; optimized version of PMID: 29651053
NEBNext Ultra II DNA Library Prep kit (New England Biolabs #E7645S)
Library strategy OTHER
Library source genomic
Library selection other
Instrument model NextSeq 2000
Description IgG
Data processing Library strategy: CUT&RUN
Base-calling: illumina software
Adapter Trimming: none
Alignment: Paired-end fastq files were aligned to the hg19 reference genome using the Bowtie2 algorithm (PMID: 22388286).
Filtering: Only uniquely aligned reads were retained, and blacklist regions (PMID: 31249361) were filtered out for subsequent analyses.
Peak Calliing: Peaks were called using SEACR (Sparse Enrichment Analysis of CUT&RUN) (PMID: 31300027).
Genome_build: hg19
Supplementary_files_format_and_content: Musselman_Metadata.xlsx: contains one excel sheet
Submission date Jul 14, 2021
Last update date Jul 16, 2021
Contact name Bryan J Venters
Organization name EpiCypher
Street address 6 Davis Drive
City Durham
State/province NC
ZIP/Postal code 27709
Country USA
Platform ID GPL30173
Series (1)
GSE150617 Nucleosome conformation dictates the histone code
BioSample SAMN20209552
SRA SRX11439583

Supplementary file Size Download File type/resource 38.0 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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