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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 31, 2017 |
| Title |
M10P ATAC-Seq |
| Sample type |
SRA |
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| Source name |
M10P organoid
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: Mouse PDA peritoneum metastasis (M10P)
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| Growth protocol |
Mouse/human PDA organoids or cell lines were cultured in conditions as described in this study.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclear extract were prepared from 50,000 single cell dissociated of organoid cultures, incubated with Tn5 transposase, and purified with Qiagen MinElute kit for library construction.
Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit, as originally described in Buenrostro et al. (2013).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Raw reads were mapped to the reference mouse (mm9) genome assembly using Bowtie allowing two-mismatches for only unique alignment; -v 2 -m 1 -best --strata. To avoid clonal artifacts introduced in the library amplification steps, duplicated mapped reads were further discarded using SAMtools (http://samtools.sourceforge.net).
HOMER suite (http://homer.salk.edu/homer/) was used for overall analysis. Details were described in the experimental procedues of this study.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig
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| Submission date |
May 24, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jae Seok Roe |
| E-mail(s) |
jroe@yonsei.ac.kr
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| Organization name |
Yonsei University
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| Street address |
Yonsei-ro, 50
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| City |
Seoul |
| ZIP/Postal code |
03722 |
| Country |
South Korea |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE99275 |
Enhancer reprogramming promotes pancreatic cancer progression and metastasis [ATAC-seq] |
| GSE99311 |
Enhancer reprogramming promotes pancreatic cancer progression and metastasis |
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| Relations |
| BioSample |
SAMN07163687 |
| SRA |
SRX2852943 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2640278_M10P_ATAC.bigWig |
275.9 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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