|
| Status |
Public on Nov 06, 2024 |
| Title |
Paf1 cKO ser2p CUT&Tag rep2 |
| Sample type |
SRA |
| |
|
| Source name |
DP thymocytes
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Paf1 cKO (Paf1F/F;Lck+)
antibody: ser2p
|
| 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 |
Paf1_cKO.ser2p.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 |
GPL24247 |
| Series (2) |
| GSE188412 |
The PAF1 Complex Regulates Transcriptional Termination and Reinitiation [CUT&Tag] |
| GSE188417 |
The PAF1 Complex Regulates Transcriptional Termination and Reinitiation |
|
| Relations |
| BioSample |
SAMN22984458 |
| SRA |
SRX13057071 |
