|
| Status |
Public on Aug 06, 2020 |
| Title |
iHep_4a3_2_Foxa3 |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
transfection: infected with Foxa3, Hnf4alpha
Stage: iHep
antibody: Foxa3
|
| Treatment protocol |
ChIP-seq experiments were carried out following standard procedures in iHep cells or hepatocytes.
|
| 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). Hepatocytes were isolated from 10-week-old adult mouse livers by two-step collagenase digestion (Seglen, 1979).
|
| 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 NovaSeq 6000 |
| |
|
| 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 |
Jan 15, 2020 |
| 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 |
GPL24247 |
| Series (1) |
| GSE90538 |
Foxa and Hnf4alpha targets during conversion from mouse embryonic fibroblasts (MEFs) to hepatocyte-like (iHep) cells and hepatocytes (Hep). |
|
| Relations |
| BioSample |
SAMN13869915 |
| SRA |
SRX7569431 |
