|
| Status |
Public on Jan 30, 2023 |
| Title |
H3K27ac, WCM1262, Organoid, Input |
| Sample type |
SRA |
| |
|
| Source name |
Neuroendocrine prostate cancer
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Neuroendocrine prostate cancer
cell line: Not applicable
cell type: NEPC organoid
genotype: Wild Type
treatment: Not applicable
|
| Treatment protocol |
Not applicable
|
| Growth protocol |
The NEPC organoids were combined with growth factor-reduced Matrigel (Corning) in a 1:2 volume ratio. Six droplets of 50 μl cell suspension/Matrigel mixture was pipetted onto each well of a six-well cell suspension culture plate (Greiner). The 6-well plate was placed into a cell culture incubator at 37 °C and 5% CO2 for 30 min to solidify the droplets before 2.5 ml of prostate-specific culture media was added to each well. The organoids were grown in prostate-specific culture media composed of Advanced DMEM/F12 (Invitrogen) with GlutaMAX (1×, Invitrogen), HEPES Buffer (1M, Invitrogen), 100 U/ml penicillin, 100 μg/ml streptomycin (Gibco), B27 supplement (Gibco), N-Acetylcysteine 1.25 mM (Sigma-Aldrich), Mouse Recombinant protein EGF 50 ng/ml (Peprotech), Human Recombinant FGF-10 20 ng/ml (Peprotech), Recombinant Human FGF-basic 1 ng/ml (Peprotech), A-83-01 500 nM (Tocris), SB202190 10 μM (Sigma-Aldrich), Nicotinaminde 10 mM (Sigma-Aldrich), PGE2 1 μM (Tocris), NRG 100 μl/ml (GenScript), Y-27632-2HC1 10µM (Selleck), Noggin conditioned media (10%) and R-spondin conditioned media (5%). The culture was replenished with fresh media every 3−4 days during organoid growth. Dense cultures with organoids ranging in size from 200 to 500 um were passaged every 10 to 12 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells was fixed using 1% formaldehyde and chromatin sheared to 300-500 bp in size using the Covaris E220 ultrasonicator. Resulting chromatin was incubated overnight with indicated antibodies. Purified immunoprecipitates were isolated and quantified by Qubit fluorometer. DNA sequencing libraries were prepared using the ThruPLEX-FD Prep kit (Rubicon Genomics). Libraries were sequenced using 75-bp reads on the Illumina platform at the Dana-Farber Cancer Institute.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
H3K27ac_Input_WCM1262
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Reads were aligned to mm9 using BWA
For peak calling MACS2 was used.
Assembly: hg19
Supplementary files format and content: bw files were generated using MACS2 using the chilin pipeline
|
| |
|
| Submission date |
Dec 22, 2022 |
| Last update date |
Jan 30, 2023 |
| Contact name |
Himisha Beltran |
| E-mail(s) |
himisha_beltran@dfci.harvard.edu
|
| Phone |
6175829421
|
| Organization name |
Dana Farber Cancer Institute
|
| Department |
Department of Medical Oncology
|
| Street address |
450 Brookline Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE211452 |
Landscape of prostate-specific membrane antigen heterogeneity and regulation in AR-positive and AR-negative metastatic prostate cancer |
| GSE221613 |
Landscape of Prostate-Specific Membrane Antigen Heterogeneity in Metastatic Prostate Cancer [ChIP-Seq] |
|
| Relations |
| BioSample |
SAMN32372480 |
| SRA |
SRX18827413 |
