|
| Status |
Public on Apr 23, 2019 |
| Title |
Input adult acinar cells 2 |
| Sample type |
SRA |
| |
|
| Source name |
adult acinar cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl6/J wildtype
cell type: adult acinar cells
chip antibody: Input
|
| Treatment protocol |
Acinar-to-ductal metaplasia was additionally treated with 50 ng/ml Tgf-alpha.
|
| Growth protocol |
Embryonic acinar cells and adult acinar cells from C57Bl6/J wildtype mice were freshly isolated by collagen-digestion and directly used for DNA extraction. Adult acinar cells were additionally cultivated in 3D-collagen for 7 days, undergoing acinar-to-ductal metaplasia. Low-passage tumor cells, isolated from a conditional mutant Kras-driven pancreatic cancer mouse model, were grown in standard medium.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After formalin fixation, fragmented DNA was precipitated with specific antibodies, reverse-crosslinked and extracted with a PCR purification kit from Qiagen according to the manufacture´s instructions.
NEBNext Ultra DNA Library Prep Kit for Illumina according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
L10843_Track-31231_R1
|
| Data processing |
Paired-end reads were mapped to M. musculus genome assembly mm10. We used Bowtie v1.1.2 with “-m 1” parameter setting.
Mapped eads were extended to 200bp prior to calculating genome-wide coverage
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files with genome-wide fragment coverage
|
| |
|
| Submission date |
Jun 22, 2018 |
| Last update date |
Apr 23, 2019 |
| Contact name |
Tobias Straub |
| E-mail(s) |
tstraub@med.uni-muenchen.de
|
| Organization name |
LMU Munich
|
| Department |
Biomedical Center, Bioinformatics
|
| Street address |
Großhadener Str. 9
|
| City |
Martinsried |
| ZIP/Postal code |
82152 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE116151 |
Dynamic changes in the epigenetic landscape are mandatory for acinar cell reprogramming and pancreatic carcinogenesis [ChIP-seq] |
| GSE116152 |
Dynamic changes in the epigenetic landscape are mandatory for acinar cell reprogramming and pancreatic carcinogenesis |
|
| Relations |
| BioSample |
SAMN09469934 |
| SRA |
SRX4283028 |
