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Sample GSM4171607 Query DataSets for GSM4171607
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 (
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
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
BioSample SAMN13293655
SRA SRX7157505

Supplementary file Size Download File type/resource
GSM4171607_WT_Rbpj.AUC_peaks.bed.gz 104.3 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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