|Public on May 06, 2022
|MEF cells - input DNA_rep3
|chip antibody: whole cell extract
cell line/type: Mouse embryonic fibroblast (MEF)
|MEFs were infected with lentiviral particles carrying AM-tagged Atoh8.
|MEFs were isolated from E13.5 embryos after removal of the head and internal organs. The remaining tissues were physically dissociated and incubated in trypsin at 37°C for 10 min after which cells were resuspended in MEF medium.
|After 3 days, DNA was extracted, precipitated and purified using the Tag-ChIP-IT kit (53022, Actif Motif).
Libraries were prepared according to Illumina's instructions.
|Illumina HiSeq 2500
|Atoh8 and Bcl11b ChIP-sequencing datasets were aligned to the mouse reference genome assembly mm10 using Bowtie 2.1.0 under by default parameters
Peak calling was performed using MACS 2.1.1. Atoh8-specific sites were obtained by subtracting binding sites observed within the AM-tag processed control dataset (BEDTools 2.29.2).
Enrichment heat maps and mean density plots were obtained with seqMINER. De novo motif analysis has been performed with MEME-ChIP
Read counts enrichment signals were visualized with IGV genome browser. Genome_build: mm10
Supplementary_files_format_and_content: Peak calling was performed using MACS 2.1.1. In addition, bedgraphs were also generated at this stage for genome browser visualization (IGV).
Supplementary_files_format_and_content: bedgraph files (MACS 2.1.1.)
Supplementary_files_format_and_content: Peak list files (MACS 2.1.1.)
|Mar 06, 2022
|Last update date
|May 06, 2022
|28 rue Laennec
|The comparative roadmaps of reprogramming and transformation unveiled that cellular plasticity is broadly controlled by Bcl11b and Atoh8
|Bcl11b and Atoh8 binding on chromatin in MEFs