|
| Status |
Public on Nov 01, 2025 |
| Title |
LS174T-R_H3K4me3,LS174T resistant, H3K4me3 ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
LS174T
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LS174T
cell type: human colorectal adenocarcinoma cell line
genotype: KRAS mutant (G12D)
treatment: BI-2866
batch: 3
|
| Treatment protocol |
Resistant models were generated by chronic exposure to increasing concentrations of BI-2865 pan-KRAS inhibitor. For ChIP-seq experiments, cells were treated with 5μM BI-2865 or DMSO control for 24 hours.
|
| Growth protocol |
LS174T and other commercial CRC cell lines were cultured in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin at 37°C in 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Mini Kit (Qiagen). For ChIP-seq, chromatin was cross-linked with 1% formaldehyde, sonicated, and immunoprecipitated with H3K27ac (Abcam ab4729) or H3K4me3 (Millipore 07-473) antibodies.
RNA-seq libraries were prepared with TruSeq Stranded RNA HT kit with Ribo-Zero Gold (Illumina). ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Library name: Sample12
|
| Data processing |
Quality control: FastQC v0.11.8. Adapter trimming: Trim Galore v0.6.3.
RNA-seq alignment: STAR v2.7.9a to GRCh37 (hg19) reference genome.
ChIP-seq alignment: BWA-MEM v0.7.17 to GRCh37 (hg19) reference genome.Peak calling: MACS2 v2.1.2 for H3K27ac and H3K4me3 peaks.
Differential expression: DESeq2 v1.28.1 for RNA-seq data.
Assembly: GRCh37 (hg19)
Supplementary files format and content: tab-delimited text files containing raw counts and normalized expression values for RNA-seq
|
| |
|
| Submission date |
Sep 02, 2025 |
| Last update date |
Nov 01, 2025 |
| Contact name |
yao yu Guo |
| E-mail(s) |
guoyy@mail2.sysu.edu.cn
|
| Organization name |
Sun-Yat san university
|
| Street address |
广州
|
| City |
广州 |
| ZIP/Postal code |
775028 |
| Country |
China |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE306909 |
Enhancer Remodeling-Driven Mevalonate Pathway Confers Resistance to KRAS Inhibitor in Colorectal Cancer |
|
| Relations |
| BioSample |
SAMN50912818 |
| SRA |
SRX30320317 |
