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Sample GSM3940104 Query DataSets for GSM3940104
Status Public on Jul 11, 2020
Title Foxa2+KrasG12D_ChIP
Sample type SRA
 
Source name pancreatic adenocarcinoma
Organism Mus musculus
Characteristics cell type: pancreatic adenocarcinoma cancer Tet-on KrasG12D cell line
strain: B6/FVB
chip antibody: anti-Foxa2 (Cell Signaling, #8186)
Treatment protocol To KrasG12D cell line: +KrasG12D means treatment with Dox;-KrasG12D means No Dox add.PDA cell line:+KrasG12D means endogenous KrasG12D expression.
Growth protocol To KrasG12D cell line: DMEM+10%FBS+1%P/S+1ug/ml Doxycycline; PDA cell line:DMEM+10%FBS+1%P/S
Extracted molecule genomic DNA
Extraction protocol Briefly, cells were crosslinked at room temperature for 10 min with 1% formaldehyde, washed twice with PBS and sonicated in lysis buffer (50 mM HEPES/KOH pH 7.5, 140 mM NaCl, 0.1% Na-Deoxycholate, 1% Triton X-100, 1 mM EDTA, complete protease inhibitor cocktail). Samples were immunoprecipitated at 4 ºC overnight and washed six times with ChIP wash buffer (20 mM Tris, pH 7.9, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS) and once with TE buffer. Bound DNA was eluted in 1% SDS buffer and reverse-crosslinked for 6 h at 65 ºC
DNA samples were treated sequentially with RNase A and Protease K and then purified with ChIP DNA Clean & Concentrator-5 (Zymo Research, D4014)
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model HiSeq X Ten
 
Data processing The adapters of paired-end reads were trimmed and quality control checks were carried out using trim-galore (version 0.6.0). Trimmed reads were aligned to mouse genome reference (GRCm38.p6) from GENCODE using bowtie2 (version 2.3.4.3) of which the parameter is “–very-sensitive –X 2000”. Aligned reads stored in SAM format were manipulated to generate bam files using samtools (version 1.9) with parameter is “samtools view –b –h –F 1028 –f 3”. Peaks of ChIP-seq were called using MACS2 (version 2.1.2) using the parameter “macs2 callpeak --verbose 3 -g mm -B -q 1e-3 -f BEDPE”. Analysis of differential peaks intensity was processed using MAnorm (version 1.1.4).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using deeptools
 
Submission date Jul 12, 2019
Last update date Jul 12, 2020
Contact name Yi He
E-mail(s) sonichy@126.com
Organization name Tsinghua university
Street address 30 Shuangqing Rd, Haidian Qu, Beijing Shi, China
City Beijing
ZIP/Postal code 100084
Country China
 
Platform ID GPL21273
Series (2)
GSE134233 Mutant Kras co-opts a progenitor-derived enhancer network to initiate pancreatic tumorigenesis [ChIP-seq]
GSE134236 Mutant Kras co-opts a progenitor-derived enhancer network to initiate pancreatic tumorigenesis
Relations
BioSample SAMN12264433
SRA SRX6437841

Supplementary file Size Download File type/resource
GSM3940104_Foxa2+KrasG12D_ChIP.bw 108.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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