|
| Status |
Public on Jan 16, 2024 |
| Title |
BRD4_FLAG_T2_2 |
| Sample type |
SRA |
| |
|
| Source name |
day 6 human iPSC-derived cardiac progenitor cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: WTC11 hIPSCs
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were isolated with Nuclear extraction buffer [20 mM HEPES-KOH, pH 7.9, 10 mM KCl, 0.5 mM Spermidine (Sigma #05292–1ml-F), 0.1% Triton X-100, 20% Glycerol and 1× protease and phosphatase inhibitor (Thermo Fisher #78442)]. To aid in nuclear capture, isolated nuclei were incubated with activated Concanavalin A beads (Bangs Laboratories #Bp531) for 15 minutes at room temperature followed by incubation with the desired primary antibody (1:100 dilution) overnight.
Libraries were prepares using a commercially available CUT&RUN kit (Epicypher #14-1048).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
WTC11 hIPSCs differentiated to cardiac progenitor cells (CPCs) with CUT&RUN performed on day 6
BRD4_FLAG_T2rep1+2_mean_SEACR_FDR1e-2.bed
|
| Data processing |
library strategy: Cleavage Under Target & Release (CUT&RUN)
Illumina Casava v1.8 was used for base-calling.
All Cut & Run raw data was initially processed using the nfcore Cut & Run pipeline (nf-core/cutandrun v2.0) with standard settings, aligned to hg38.
Peaks were called outside of nfcore framework using Sparse Enrichment Analysis for CUT&RUN (SEACR v1.3) with an FDR threshold of 1e-2
Assembly: hg38
Supplementary files format and content: Bed files of SEACR peak calls from IgG subtracted and averaged samples (FDR threshold 0.01)
|
| |
|
| Submission date |
Jan 16, 2024 |
| Last update date |
Jan 16, 2024 |
| Contact name |
Angelo Pelonero |
| E-mail(s) |
angelo.pelonero@gladstone.ucsf.edu
|
| Organization name |
Gladstone Institutes (UCSF)
|
| Department |
Cardiovascular Disease Institute
|
| Lab |
Srivastava Lab
|
| Street address |
1650 Owens Street
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE184922 |
A Genome-Wide CRISPR Screen Identifies BRD4 as a Regulator of Cardiomyocyte Differentiation |
| GSE253329 |
A Genome-Wide CRISPR Screen Identifies BRD4 as a Regulator of Cardiomyocyte Differentiation [CUT&RUN] |
|
| Relations |
| BioSample |
SAMN39458817 |
| SRA |
SRX23230933 |
