|
| Status |
Public on Jul 11, 2020 |
| Title |
KrasG12D_D2_R1_ATAC-seq |
| Sample type |
SRA |
| |
|
| Source name |
ADM
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6/FVB
genotype: Pdx1-cre;Klf5-mCherry-CreERT2;LSL-KrasG12D;R26RLSL-YFP
days after injection: day 2
|
| 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 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 |
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) |
| 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 |
SAMN12264380 |
| SRA |
SRX6437827 |
