|
| Status |
Public on May 16, 2018 |
| Title |
I_WT_Input |
| Sample type |
SRA |
| |
|
| Source name |
Pancreas
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Pancreas
strains: C57BL/6
antibody: none
genotype/variation: WT
treatment: NoCaerulein
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Purified ChIP DNA (5 ng per sample) was used for generation of sequencing libraries with TruSeq ChIP Sample Prep Kit (Illumina).
The resultant DNA libraries were assessed on an Agilent Bioanalyzer and quantified with KAPA Library Quantification Kits (KAPA BIOSYSTEMS). The libraries were sequenced to generate single-end 86 bp reads using NextSeq 500 (illumina).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
WT Pancreas NoCaerulein M Input
|
| Data processing |
The low-quality bases at the 3' read ends and the adaptors were trimmed using cutadapt-1.9.1. Untrimmed and trimmed reads of 20 bp or longer were mapped to mouse genome (mm10) with BWA 0.7.12 with default setting.
Duplicate reads and low mapping quality reads (MAPQ < 20) were removed using Picard and SAMtools.
To handle male and females samples equally, the data on chromosome X and Y were excluded for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bw (bigwig) *The data were normalized as RPM (reads per million)
|
| |
|
| Submission date |
Mar 02, 2018 |
| Last update date |
May 16, 2018 |
| Contact name |
Yasuhiro Yamada |
| E-mail(s) |
yyamada@m.u-tokyo.ac.jp
|
| Organization name |
University of Tokyo
|
| Department |
Department of Molecular Pathology
|
| Street address |
7-3-1 Hongo, Bunkyo-ku
|
| City |
Tokyo |
| ZIP/Postal code |
113-0033 |
| Country |
Japan |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE100841 |
In vivo reprogramming drives Kras-induced cancer development [ChIP-seq] |
| GSE100842 |
In vivo reprogramming drives Kras-induced cancer development |
|
| Relations |
| BioSample |
SAMN08630911 |
| SRA |
SRX3757268 |
