|
| Status |
Public on Jul 31, 2017 |
| Title |
KPC-2D/FOXA1 FOXA1 ChIP-Seq (rep2) |
| Sample type |
SRA |
| |
|
| Source name |
KPC-2D/FOXA1 cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: Monolayer-cultured cells established from mouse PDA primary tumor organoid (T3)
peturbation: Transduced with MSCV/FOXA1 retrovirus
biological replicate: rep2
antibody: FOXA1 (ab23738; Abcam)
|
| Treatment protocol |
For cDNA overepxression, cDNAs were retrovirally introduced and selected with G418. For shRNA expression, shRNAs were retrovirally introduced and selected with puromycin. For sgRNA expression, sgRNAs were lentivirally introduced and GFP-sorted with FACS.
|
| Growth protocol |
Mouse/human PDA organoids or cell lines were cultured in conditions as described in this study.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were prepared from ~1 millon single cell dissociated of organoid cultures, or ~5 million of monolayer cultures. Sonicated nuclei with Bioruptor were further proceeded to ChIP assay with apporiate antibodies.
Libraries were prepared according to Illumina's instructions of TruSeq ChIP Sample Prep kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Raw reads were mapped to the reference mouse (mm9) or human (hg19) 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: mm9 and hg19
Supplementary_files_format_and_content: bigWig
|
| |
|
| Submission date |
May 24, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jae Seok Roe |
| E-mail(s) |
jroe@yonsei.ac.kr
|
| Organization name |
Yonsei University
|
| Street address |
Yonsei-ro, 50
|
| City |
Seoul |
| ZIP/Postal code |
03722 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE99284 |
Enhancer reprogramming promotes pancreatic cancer progression and metastasis [ChIP-seq] |
| GSE99311 |
Enhancer reprogramming promotes pancreatic cancer progression and metastasis |
|
| Relations |
| BioSample |
SAMN07163983 |
| SRA |
SRX2853324 |
