|
| Status |
Public on Jul 09, 2021 |
| Title |
H7_1: H7 tumor ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
PANC02-H7 orthotopic tumors from tumor-bearing mice
|
| Organism |
Mus musculus |
| Characteristics |
tissue: PANC02-H7 orthotopic tumor
site: Pancreas
replicates: Replicate 1
|
| Growth protocol |
PANC02-H7 and UN-KC-6141 cells were surgically injected to pancrease of C57BL/6 mice. Tumors were dissected from mice 20 days after tumor cell injection.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Normal mouse pancreas and tumors from tumor-bearing mice were used for chromatin fragment preparation. Anti-H3K4me3 antibody was used for ChIP, followed by library construction and ChIP-sequencing.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ChIP DNA
|
| Data processing |
The ChIP-seq analysis was performed on Galaxy server. Adaptor and quality trimming were performed using Trim Glore! Modules (Galaxy v0.4.3.1). Trimmed reads were mapped to mouse genome mm10 using Bowtie2 (Galaxy v2.3.4.3) using default settings. Reads mapped to the mitochondria genome were removed using Filter SAM or BAM function under the samtools module (Galaxy v1.8), and PCR duplicates were removed using MarkDuplicates from Picard tool v2.20.2. The mapped reads overlapping with ENCODE blacklist regions (version 2) were filtered before calling peaks.
ChIP-seq peak calling was performed on Galaxy server using MACS2 v2.1.2 using default settings”.
DiffBind (Galaxy v. 2.6.6.4) was used to identify differential peaks.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig
|
| |
|
| Submission date |
Jun 22, 2021 |
| Last update date |
Jul 09, 2021 |
| Contact name |
Huidong Shi |
| E-mail(s) |
[email protected]
|
| Phone |
706-721-6000
|
| Organization name |
Augusta University
|
| Department |
Georgia Cancer Center
|
| Lab |
2125 K
|
| Street address |
1120 15th Street, CN2138
|
| City |
Augusta |
| State/province |
GA |
| ZIP/Postal code |
30912 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE178675 |
The WDR5-H3K4me3 epigenetic axis regulates OPN expression to compensate PD-L1 function to promote pancreatic cancer immune escape [ChIP-seq] |
| GSE178677 |
The WDR5-H3K4me3 epigenetic axis regulates OPN expression to compensate PD-L1 function to promote pancreatic cancer immune escape |
|
| Relations |
| BioSample |
SAMN19813735 |
| SRA |
SRX11197090 |
