|
| Status |
Public on Feb 19, 2024 |
| Title |
H3K4me3_C_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
GCB-DLBCL
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: GCB-DLBCL
genotype: C_hom_KI
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 |
SAMN33193457 |
| SRA |
SRX19305753 |
