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Sample GSM4443913 Query DataSets for GSM4443913
Status Public on Jul 11, 2020
Title Knock_out_Kras_in_vivo_R2_ATAC-seq
Sample type SRA
 
Source name KrasG12D,KO_Cdkn2a;KO_Smad4;KO_Trp53;KO_Kras_pancreas
Organism Mus musculus
Characteristics strain background: B6/FVB
genotype: LSL-KrasG12D;Rosa26LSL-YFP;Rosa26LSL-Cas9
tissue: pancreas
cell type: eGFP-positive cells
Treatment protocol AAV injections were performed 8 days early before Caerulein injections. Caerulein injections were performed on 4 or 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.
TAM_induced* samples: Tamoxifen injections were performed 150mg/kg, four times per mouse. 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)
TAM_induced* samples: 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
 
Description pool11-A-1643_FKDL202555767-1a-DY0021-N501_H7KC2CCX2_L4
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 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 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 Mar 30, 2020
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)
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
Relations
BioSample SAMN14485944
SRA SRX8026879

Supplementary file Size Download File type/resource
GSM4443913_Knock_out_Kras_in_vivo_R2_ATAC-seq.bw 48.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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