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Sample GSM2406452 Query DataSets for GSM2406452
Status Public on Aug 06, 2020
Title iHep_4a1_2_EGS_Foxa1_R170
Sample type SRA
 
Source name mouse embryonic fibroblasts
Organism Mus musculus
Characteristics cell type: mouse embryonic fibroblasts
strain: C57BL/6
transfection: infected with Foxa1, Hnf4alpha
Stage: iHep
antibody: Foxa1
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 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 Nov 25, 2016
Last update date Aug 06, 2020
Contact name Atsushi Suzuki
Organization name Medical Institute of Bioregulation, Kyushu University
Department 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)
GSE90538 Foxa and Hnf4alpha targets during conversion from mouse embryonic fibroblasts (MEFs) to hepatocyte-like (iHep) cells and hepatocytes (Hep).
Relations
BioSample SAMN06064654
SRA SRX2379252

Supplementary file Size Download File type/resource
GSM2406452_iHep_4a1_2_EGS_Foxa1_R170_peaks.bed.gz 7.7 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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