|
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
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|
|
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.
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|
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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 |