GSE143804
GSE GEOMYC ChIP-seq in human pancreatic ductal adenocarcinoma cells
Organism:
Homo sapiens
Platform:
GPL16791
Samples:
6
Experiment Types:
Genome binding/occupancy profiling by high throughput sequencing
Submitted:
Jan 16 2020
Last Updated:
Jul 27 2020
Status:
Public on Apr 27 2020
Contact:
Mara,,Sherman (Oregon Health & Science University)
Relations
BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA601741
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP242235
Summary
To assess modulation of global MYC chromatin occupancy by stromal cues, we exposed human pancreatic cancer cells to secreted factors from cancer-associated fibroblasts and performed ChIP-seq in stroma-stimulated cells compared to controls.
Overall Design
MIAPaCa2 human PDAC cells were serum-starved for 48 hours, then treated with fresh serum-free media or with serum-free conditioned media from primary cancer-associated fibroblasts. After 3 hours, cells were fixed and ChIP for MYC performed.
Analysis (9 steps)
View Data Processing
Processing steps for GSE143804
- Reads trimmed using default paramters of Trim Galore!
- Version 0.4.3
- Trimmed reads aligned to human reference genome GRCh38, release 87 using bowtie2 (version 2.3.4)
- Alignments filtered for reads with MAPQ score >= 11 using samtools (version 1.3.1)
- Duplicates removed using picard tools (version 2.9.0)
- Peaks called using MACS2 (version 2.1.1.20160309)
- Peaks filtered for known chromosomes only
- common peaks shared between replicates determined by findOverlapsOfPeaks() from ChIPpeakAnno R package (version 3.14.2)
Showing first 8 steps.
Supplementary Files (4)
GEO Samples (6)
Dataset Citations (1)
SRA Experiments (6) and Runs (6)
Total: 8234 MBGSM4274816: CM_Input_S24; Homo sapiens; ChIP-Seq
Sample: SRS6007672
BioProject: PRJNA601741
BioSample: SAMN13872934
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: conditioned media
cell line: MIAPaCa2
cell type: Pancreatic ductal adenocarcinoma
chip antibody: Cell Signaling Technology MYC Antibody #9402
Original files (1)
conditioned media
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR10903933 | 31212378 | 3152450178 | 1356.64 | CM_Input_S24_reads.fastq.gz, SRR10903933, SRR10903933.sralite | SRA |
GSM4274817: CM_IP_1_S28; Homo sapiens; ChIP-Seq
Sample: SRS6007673
BioProject: PRJNA601741
BioSample: SAMN13872933
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: conditioned media
cell line: MIAPaCa2
cell type: Pancreatic ductal adenocarcinoma
chip antibody: Cell Signaling Technology MYC Antibody #9402
Original files (1)
conditioned media
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR10903934 | 31699289 | 3201628189 | 1390.2 | CM_IP_1_S28_reads.fastq.gz, SRR10903934, SRR10903934.sralite | SRA |
GSM4274818: CM_IP_2_S29; Homo sapiens; ChIP-Seq
Sample: SRS6007674
BioProject: PRJNA601741
BioSample: SAMN13872932
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: conditioned media
cell line: MIAPaCa2
cell type: Pancreatic ductal adenocarcinoma
chip antibody: Cell Signaling Technology MYC Antibody #9402
Original files (1)
conditioned media
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR10903935 | 31016619 | 3132678519 | 1361.04 | CM_IP_2_S29_reads.fastq.gz, SRR10903935, SRR10903935.sralite | SRA |
GSM4274819: DMEM_Input_S23; Homo sapiens; ChIP-Seq
Sample: SRS6007675
BioProject: PRJNA601741
BioSample: SAMN13872931
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: DMEM
cell line: MIAPaCa2
cell type: Pancreatic ductal adenocarcinoma
chip antibody: Cell Signaling Technology MYC Antibody #9402
Original files (1)
DMEM
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR10903936 | 30971224 | 3128093624 | 1341.59 | DMEM_Input_S23_reads.fastq.gz, SRR10903936, SRR10903936.sralite | SRA |
GSM4274820: DMEM_IP_1_S25; Homo sapiens; ChIP-Seq
Sample: SRS6007676
BioProject: PRJNA601741
BioSample: SAMN13872930
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: DMEM
cell line: MIAPaCa2
cell type: Pancreatic ductal adenocarcinoma
chip antibody: Cell Signaling Technology MYC Antibody #9402
Original files (1)
DMEM
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR10903937 | 31558103 | 3187368403 | 1389.08 | DMEM_IP_1_S25_reads.fastq.gz, SRR10903937, SRR10903937.sralite | SRA |
GSM4274821: DMEM_IP_2_S26; Homo sapiens; ChIP-Seq
Sample: SRS6007677
BioProject: PRJNA601741
BioSample: SAMN13872929
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Homo sapiens
Sample attributes
source_name: DMEM
cell line: MIAPaCa2
cell type: Pancreatic ductal adenocarcinoma
chip antibody: Cell Signaling Technology MYC Antibody #9402
Original files (1)
DMEM
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR10903938 | 31792149 | 3211007049 | 1395.07 | DMEM_IP_2_S26_reads.fastq.gz, SRR10903938, SRR10903938.sralite | SRA |
Linked Publications (1)
A super-enhancer-regulated RNA-binding protein cascade drives pancreatic cancer.
Nature communications · 2023
Data Files (6)
| Accession | File Name | Stored Type | Output Type | Mapping Assembly | Size | Download | |
|---|---|---|---|---|---|---|---|
| — | CM_Input_S24_reads.fastq.gz | ChIP-Seq | 1.3 GB | link | |||
| — | CM_IP_1_S28_reads.fastq.gz | ChIP-Seq | 1.4 GB | link | |||
| — | CM_IP_2_S29_reads.fastq.gz | ChIP-Seq | 1.3 GB | link | |||
| — | DMEM_Input_S23_reads.fastq.gz | ChIP-Seq | 1.3 GB | link | |||
| — | DMEM_IP_1_S25_reads.fastq.gz | ChIP-Seq | 1.4 GB | link | |||
| — | DMEM_IP_2_S26_reads.fastq.gz | ChIP-Seq | 1.4 GB | link |