|
| Status |
Public on Feb 04, 2020 |
| Title |
WT |
| Sample type |
SRA |
| |
|
| Source name |
Cultured Mouse Keratinocytes
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Primary keratinocytes culture
antibody: abcam RBPJ ChIP grade Ab (cat # 25949)
|
| Treatment protocol |
EDTA for 30mins, 15 mins recovery in growth media.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Zymoresearch DNA purification kit.
DNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Cut&Run
|
| Data processing |
Library strategy: Cut&Run
Reads aligned to mm10 usingHisat2 (2.1.0) with parameters --no-spliced-alignment and --no-unal
Duplicate reads removed with Picard; Non-uniquely aligned reads removed (hisat flag ZS:i), Remove reads aligned to ambiguous chromosomes; remove reads in mm10 blacklist regions (https://www.nature.com/articles/s41598-019-45839-z).
CPM normalization using bedtools genomecov with -scale x (x = 1/million aligned reads).
IgG signal was removed from corresponding sample file using macs2 bdgcmp -m subtract and mac2 bdgpeakcall was used to call peaks.
Custom script was used to calculate area under the peaks (AUC) from bedgraph signal files.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_peaks.bed: Peak file in bed format. Column 4: Peak AUC, column 5: Peak summit pileup.
|
| |
|
| Submission date |
Nov 15, 2019 |
| Last update date |
Feb 06, 2020 |
| Contact name |
Daniel Schramek |
| E-mail(s) |
schramek@lunenfeld.ca
|
| Organization name |
Lunenfeld- Tanenbaum Research Institute
|
| Lab |
Schramek Lab
|
| Street address |
600 University Ave, Room 1080
|
| City |
Toronto |
| State/province |
ON |
| ZIP/Postal code |
M5G 1X5 |
| Country |
Canada |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE140496 |
In vivo CRISPR screens reveal NOTCH regulators suppressing Head and Neck Squamous Cell Carcinoma in mice [Cut&Run] |
| GSE140497 |
In vivo CRISPR screens reveal NOTCH regulators suppressing Head and Neck Squamous Cell Carcinoma in mice |
|
| Relations |
| BioSample |
SAMN13293655 |
| SRA |
SRX7157505 |
