|
| Status |
Public on Aug 06, 2020 |
| Title |
iHep_4a2_CA3_input |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
transfection: infected with Hnf4alpha, Foxa2 containing CTD of Foxa3
Stage: iHep
antibody: none (input)
|
| Treatment protocol |
ChIP-seq experiments were carried out following standard procedures in iHep cells.
|
| Growth protocol |
Mouse embryonic fibroblasts (MEFs) were prepared from 13.5 days post coitum embryos. iHep cells were generated and maintained following the previously described protocol (Sekiya and Suzuki, 2011).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sonicated DNA from cells was pulled down with antibody.
Libraries were prepared according to Illumina's instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
The sequence reads were aligned to the mouse reference genome assembly (NCBI37/mm9) using bwa (v0.6.2) with the option (aln -t 6).
peak finding algorithm MACS (v2.1.0) with the option (-g mm -p 0.00001).
The bedgraph files were obtained from the bam files using Bedtools (v2.16.2), then converted into the bw files.
Genome_build: mm9
Supplementary_files_format_and_content: The bed files contain the positions of the peaks that were obtained when normalizing the reads of the ChIP-Seq to the input. The bw files converted from the bedgraph files contain depth of reads.
|
| |
|
| Submission date |
Jul 18, 2018 |
| Last update date |
Aug 07, 2020 |
| Contact name |
Atsushi Suzuki |
| Organization name |
Kyushu University
|
| Department |
Medical Institute of Bioregulation
|
| Lab |
Division of Organogenesis and Regeneration
|
| Street address |
3-1-1 Maidashi, Higashi-ku
|
| City |
Fukuoka |
| State/province |
Fukuoka |
| ZIP/Postal code |
812-8582 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE117332 |
Targets of DNA binding, N-terminal, or C-terminal domain swapped mutant forms fo Foxa proteins in induced hepatocyte-like (iHep) cells. |
|
| Relations |
| BioSample |
SAMN09690371 |
| SRA |
SRX4405410 |
