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Sample GSM3939883 Query DataSets for GSM3939883
Status Public on Jul 11, 2020
Title KrasG12D_D0_R2_ATAC-seq
Sample type SRA
Source name pancreatic "normal' duct cell
Organism Mus musculus
Characteristics strain: B6/FVB
genotype: Pdx1-cre;Klf5-mCherry-CreERT2;LSL-KrasG12D;R26RLSL-YFP
days after injection: day 0
Treatment protocol Caerulein injections were performed on 6 week-old mice essentially as described (Morris et al., 2010), with 8 hourly injections of caerulein for two consecutive days, modified by using 4 μg of caerulein per injection
Extracted molecule genomic DNA
Extraction protocol Mouse pancreases were digested into single cell suspensions as previously described (Reichert et al., 2013a)
Libraries were prepared according to TruePrepTM DNA Library Prep Kit V2 for Illumina(Vazyme,TD502). ATAC-seq was performed using 3000 cells isolated from each mouse as described (Wu et al., 2016)
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model HiSeq X Ten
Data processing The adapters of paired-end reads were trimmed and a quality control check was carried out using trim-galore (version 0.6.0). Trimmed reads were aligned to mouse genome reference (GRCm38.p6) from GENCODE using bowtie2 (version 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 the parameter “samtools view –b –h –F 1028 –f 3”. ATAC-seq peaks were called using MACS2 (version 2.1.2) using the parameter “macs2 callpeak --verbose 3 -g mm -B -q 0.01 -f BAMPE --nolambda”. Raw counts of peaks in each sample were counted by featureCounts (version 1.6.3). Analysis of differential peak intensity and size factor for29 each sample were both obtained using DESeq2 (version 1.22.1). Normalized bigwig files were generated with 1/size factor using bamCoverage (version 3.2.0).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using bedtools
Submission date Jul 12, 2019
Last update date Jul 12, 2020
Contact name Yi He
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)
GSE134230 Mutant Kras co-opts a progenitor-derived enhancer network to initiate pancreatic tumorigenesis [ATAC-seq]
GSE134236 Mutant Kras co-opts a progenitor-derived enhancer network to initiate pancreatic tumorigenesis
BioSample SAMN12264381
SRA SRX6437826

Supplementary file Size Download File type/resource 40.8 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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