|
| Status |
Public on Aug 06, 2020 |
| Title |
48hr_4a3_del2_Foxa3_del2-x3Ty1 |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
transfection: infected with Foxa3 del2 mutant fused with x3Ty1-tag, Hnf4alpha
Stage: iHep
antibody: Ty1-tag
|
| Treatment protocol |
ChIP-seq experiments were carried out following standard procedures in iHep cells or MEFs 48 hours after transfection with retroviruses.
|
| 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 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) |
| GSE90536 |
Foxa and Hnf4alpha targets during conversion from mouse embryonic fibroblasts (MEFs) to hepatocyte-like (iHep) cells |
|
| Relations |
| BioSample |
SAMN13869899 |
| SRA |
SRX7569429 |
