|
| Status |
Public on Jul 14, 2021 |
| Title |
CUT&RUN H3K4me3 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: anti-H3K4me3 ThermoFisher #PA5-27029, lot SG2419844A
|
| 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 |
H3K4me3
|
| 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 |
|
| Relations |
| BioSample |
SAMN20209548 |
| SRA |
SRX11439585 |
