|
| Status |
Public on May 06, 2024 |
| Title |
ChIP-seq, H3K9me3, 2205 in vitro, AG120, Replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
cholangiocarcinoma
|
| Organism |
Mus musculus |
| Characteristics |
tissue: cholangiocarcinoma
cell line: 2205
cell type: tumor cells
genotype: Albumin-Cre; KrasG12D; IDH1R132C
treatment: AG120
|
| Treatment protocol |
This study used the mIDH inhibitor, AG120 (Servier Pharmaceuticals). Murine ICC (2205) cells were treated for five days with either DMSO or 1 μM mIDH inhibitor (AG120). Where indicated, 10ng/mL IFNγ was added for the final two days of culturing.
|
| Growth protocol |
Murine IDH1R132C ICC cell line (2205) were cultured in RPMI 1640 (+) L-glutamine, 25 mmol/L HEPES containing 10% FBS and 1% penicillin–streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
20 million cells per replicate for each condition (DMSO, AG120, IFNγ, AG120 + IFNγ) were cross-linked using 1% formaldehyde for 10 minutes at room temperature and quenched using glycine for 5 minutes. ChIP experiments were performed using SimpleChIP Enzymatic Chromatin IP Kit based on manufacturer's protocol.
Sequencing libraries were prepared using the NEBNext Ultra II DNA library preparation kit (New England Biolabs)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
A_H3K9me3.bw
|
| Data processing |
Fastq files were preprocessed using fastp.
Reads were mapped to mm10 using bowtie2
Duplicates were removed using Picard MarkDuplicates.
For sharp histone modification peaks seen in H3K4me3, we used MACS2 for peak-calling over input control with a parameter of -q 0.01.
For H3K9me3 and H3K27me3, peaks were first called using SICER2 with parameters of -w 200 -rt 1 -f 150 -egf 0.74 -fdr 0.01 (default settings).
To better represent the characteristics of broad histone modification of these markers, we removed peaks of less than 5 kb in length, and then merged neighboring peaks separated by less than 20 kb into one domain
For visualization, bam files were merged by replicates, normalized using scaling factor from trimmed mean of M (TMM) values from edgeR, and smoothed by 150-bp sliding windows with 20-bp bin size using bamCoverage.
Assembly: mm10
Supplementary files format and content: bigWig files for samples merged by replicates
|
| |
|
| Submission date |
May 06, 2024 |
| Last update date |
May 06, 2024 |
| Contact name |
Robert Manguso |
| E-mail(s) |
rmanguso@broadinstitute.org
|
| Organization name |
Broad Institute of MIT and Harvard
|
| Street address |
75 Ames Street
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE264730 |
Mutant IDH1 inhibition induces dsDNA sensing to activate tumor immunity |
| GSE266686 |
Mutant IDH1 inhibition induces dsDNA sensing to activate tumor immunity [ChIP-Seq] |
|
| Relations |
| BioSample |
SAMN41234087 |
| SRA |
SRX24468492 |
