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| Status |
Public on Jul 11, 2020 |
| Title |
H3K4me-KrasG12D_ChIP |
| Sample type |
SRA |
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| Source name |
pancreatic adenocarcinoma
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| Organism |
Mus musculus |
| Characteristics |
cell type: pancreatic adenocarcinoma cancer Tet-on KrasG12D cell line
strain: B6/FVB
chip antibody: anti-H3K4me1 (ab8895)
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| Treatment protocol |
To KrasG12D cell line: +KrasG12D means treatment with Dox;-KrasG12D means No Dox add.PDA cell line:+KrasG12D means endogenous KrasG12D expression.
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| Growth protocol |
To KrasG12D cell line: DMEM+10%FBS+1%P/S+1ug/ml Doxycycline; PDA cell line:DMEM+10%FBS+1%P/S
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| 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)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
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| 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
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| Submission date |
Jul 12, 2019 |
| Last update date |
Jul 12, 2020 |
| Contact name |
Yi He |
| E-mail(s) |
sonichy@126.com
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| Organization name |
Tsinghua university
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| Street address |
30 Shuangqing Rd, Haidian Qu, Beijing Shi, China
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| City |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
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| 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 |
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| Relations |
| BioSample |
SAMN12264429 |
| SRA |
SRX6437845 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3940108_H3K4me1-KrasG12D_ChIP.bw |
89.5 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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