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Sample GSM5680980 Query DataSets for GSM5680980
Status Public on Nov 06, 2024
Title PNUTS KO ser5p CUT&Tag rep1
Sample type SRA
 
Source name K562 cell line
Organism Homo sapiens
Characteristics genotype: PNUTS knockout
antibody: ser5p
Growth protocol Human cells K562 were cultured in 90% DMEM + 10% FBS+ 2% Penicillin/Streptomycin + 2 mM L-Glutamine.
Extracted molecule genomic DNA
Extraction protocol CUT&Tag experiments were performed as previously described with minor modifications(Kaya-Okur, H.S. et al. ). Briefly, 100,000 cells were used for each experiment. Cells were bound to Concanavalin A-coated beads without fixation and chromatin opening. After primary and secondary antibodies binding, pA-Tn5 transposome binding, and tagmentation, DNA was extracted by PCI.
Library was construct by PCR, NEB Phusion(M0530L) was used as protocol.
CUT&Tag
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description PNUTS_KO.ser5p.CUTTag.bw
Data processing Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters, and subsequently aligned using bowtie2 v2.3.4.1.
Normalized aboundency in each 50-bp genomic bin were generated into bigWig file using deepTools bamCoverage command with parameter --normalizeUsing CPM.
Genome_build: Hg38 for human K562 cells, mm10 for mouse.
Supplementary_files_format_and_content: BigWig files contains normalized read count (CPM, in 50-bp bins) for merged replicates.
 
Submission date Nov 08, 2021
Last update date Nov 06, 2024
Contact name Aiwei Wu
E-mail(s) aiwei.wu@sjtu.edu.cn
Organization name Shanghai Jiao Tong University
Department School of Life Sciences and Biotechnology
Lab Ming Yu
Street address 800 Dongchuan Road
City Shanghai
State/province Shanghai
ZIP/Postal code 200240
Country China
 
Platform ID GPL24676
Series (2)
GSE188412 The PAF1 Complex Regulates Transcriptional Termination and Reinitiation [CUT&Tag]
GSE188417 The PAF1 Complex Regulates Transcriptional Termination and Reinitiation
Relations
BioSample SAMN22984473
SRA SRX13057013

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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