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Sample GSM7032043 Query DataSets for GSM7032043
Status Public on Feb 19, 2024
Title H3K4me3_K_rep1
Sample type SRA
 
Source name GCB-DLBCL
Organism Homo sapiens
Characteristics cell line: GCB-DLBCL
genotype: K_hom_KO
treatment: Ab: EpiCypher 13-0028
Growth protocol Human OCI-Ly7 cell lines were cultured in IMDM supplemented with 15% FBS, 1% L-Glutamine and 1% penicillin-streptomycin.
Extracted molecule genomic DNA
Extraction protocol Cells were immobilized to ConA beads and then subject to permeabilization, antibody binding, pAG-Mnase binding and activation, targeted chromatin digestion and release, and DNA recovery by NEB Monarch DNA Cleanup Kit according to the EpiCypher CUT&RUN Protocol.
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (NEB, E7645L) following the manufacture’s protocol.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing nfcore cutandrun version 2.0
DIffBind 3.6.1
ROSE
Assembly: hg38
Supplementary files format and content: DiffBind objects by mark (normalized to read depth)
Supplementary files format and content: DESeq2 combined objects by mark normalized to read depth at promoters
Supplementary files format and content: ROSE super enhancer calls based on WT H3K27Ac
 
Submission date Feb 07, 2023
Last update date Feb 19, 2024
Contact name Christopher Russell Chin
E-mail(s) chc2077@med.cornell.edu
Phone 3393640514
Organization name Weill Cornell
Lab Melnick Lab
Street address 413 E 69th Street, Belfer Building, BB-1462
City New York City
State/province NY
ZIP/Postal code 10021
Country USA
 
Platform ID GPL24676
Series (2)
GSE224513 Cooperative super-enhancer inactivation caused by heterozygous loss of CREBBP and KMT2D skews B-cell fate decisions and accelerates development of T-cell depleted lymphomas.
GSE224781 Cooperative super-enhancer inactivation caused by heterozygous loss of CREBBP and KMT2D skews B-cell fate decisions and accelerates development of T-cell depleted lymphomas (Cut&Run)
Relations
BioSample SAMN33193455
SRA SRX19305755

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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