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Sample GSM5935358 Query DataSets for GSM5935358
Status Public on May 06, 2022
Title MEF cells - input DNA_rep3
Sample type SRA
 
Source name MEF cells
Organism Mus musculus
Characteristics chip antibody: whole cell extract
treatment: untreated
cell line/type: Mouse embryonic fibroblast (MEF)
Treatment protocol MEFs were infected with lentiviral particles carrying AM-tagged Atoh8.
Growth protocol 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.
Extracted molecule genomic DNA
Extraction protocol 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.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Data processing 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).
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files (MACS 2.1.1.)
Supplementary_files_format_and_content: Peak list files (MACS 2.1.1.)
 
Submission date Mar 06, 2022
Last update date May 06, 2022
Contact name Fabrice Lavial
Organization name CRCL
Street address 28 rue Laennec
City Lyon
ZIP/Postal code 69008
Country France
 
Platform ID GPL17021
Series (2)
GSE137050 The comparative roadmaps of reprogramming and transformation unveiled that cellular plasticity is broadly controlled by Bcl11b and Atoh8
GSE181196 Bcl11b and Atoh8 binding on chromatin in MEFs
Relations
BioSample SAMN26490270
SRA SRX14388253

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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