|
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)
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|
|
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
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|
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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 |
SAMN20209552 |
SRA |
SRX11439583 |