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Sample GSM5081951 Query DataSets for GSM5081951
Status Public on Sep 08, 2022
Title CLL_ NOTCH1ΔPEST vector H3K27ac [P5]
Sample type SRA
 
Source name Primary CLL cells
Organism Homo sapiens
Characteristics patient: P5
diagnosis: Chronic lymphocytic leukemia
cell type: Primary CLL cells from peripheral blood
genotype/variation: NOTCH1<delta>PEST
chip antibody: H3K27ac antibody, Diagenode: C15410196 /pAb-196-050 (LOT: A1723-0041D)
Treatment protocol Cells were crosslinked with 1% formaldehyde, 15 minutes at 4º. Reaction was stopped with 1.25 M glycine for 5 minutes.
Extracted molecule genomic DNA
Extraction protocol ChIP-seq were generated as described: http://www.blueprint-epigenome.eu/index.cfm?p=7BF8A4B6-F4FE-861A-2AD57A08D63D0B58
Libraries were constructed using the Kapa Hyper Prep Kit as previously described (https://www.blueprint-epigenome.eu/UserFiles/File/Protocols/Blueprint_Kapa_hyper_prep_kit.pdf).
SE, 50bp
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Description P5_NOTCH
Data processing Raw fastq files alignment using bwa 0.7.7, picard & samtools.
Wiggle plots generation using PhantomPeakQualTools.
Narrow peak calling using MACS2 callpeak function with q-value < 0.01 and without input control.
Genome_build: GRCh38.p3
Supplementary_files_format_and_content: *.bed: Bed files describing the location of the peaks.
 
Submission date Feb 13, 2021
Last update date Sep 08, 2022
Contact name Irina Mohorianu
E-mail(s) data-submissions@stemcells.cam.ac.uk
Organization name University of Cambridge
Department Wellcome-MRC Cambridge Stem Cell Institute
Street address Puddicombe Way
City Cambridge
ZIP/Postal code CB2 0AW
Country United Kingdom
 
Platform ID GPL24676
Series (2)
GSE150610 Gene expression profile of primary CLL cells transduced with a mutated NOTCH1
GSE166727 Histone H3 lysine 27 acetylation (H3K27ac) profile of primary CLL cells transduced with a retrovirus expressing mutated NOTCH1
Relations
BioSample SAMN17910342
SRA SRX10095002

Supplementary file Size Download File type/resource
GSM5081951_P5_NOTCH.bed.gz 964.3 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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