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Sample GSM4287326 Query DataSets for GSM4287326
Status Public on May 13, 2021
Title H3K27ac_SAMD1KO
Sample type SRA
Source name E14TG2a
Organism Mus musculus
Characteristics antibody: H3K27ac (Active Motif, 39133)
genotype: SAMD1KO
cell line: E14TG2a
Growth protocol E14 mouse ES cells (E14TG2a) were cultured in DMEM, 15% FCS, 1 x L-Glutamine, 1 x Non-essential amino acids, 1 x Sodium pyruvate, 1 x Penicillin/Streptomycin , 0.15% β-mercaptoethanol and 100 Units/ml of LIF on gelatin-coated plates.
Extracted molecule genomic DNA
Extraction protocol ChIP experiments were performed in accordance to the One Day ChIP kit protocol (Diagenode). Total RNA was extracted by using the RNeasy Mini system (Qiagen) including an on-column DNaseI digestion.
For ChIP-Seq library five nanograms of precipitated DNA were used for indexed sequencing library preparation using the Microplex library preparation kit v2 (Diagenode). RNA-Seq libraries were prepared using the TruSeq Stranded mRNA Library Prep kit (Illumina).
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model NextSeq 550
Data processing ChIP-Seq data were aligned to mouse genome mm9, mm10 or dm6 (spike-in) using Bowtie 1.0, allowing one mismatch.
SAM files were converted to bigwig files using SamTools, and deepTools/bamCoverage. Data were normalized to RPKM and spike-in control.
Genome_build: mm9, mm10, dm6
Supplementary_files_format_and_content: bw
Submission date Jan 28, 2020
Last update date May 13, 2021
Contact name Robert Liefke
Organization name Philipps University of Marburg
Department Institute of Molecular Biology and Tumor Research (IMT)
Street address Hans-Meerwein-Str. 2
City Marburg
State/province Hessen
ZIP/Postal code 35043
Country Germany
Platform ID GPL21626
Series (1)
GSE144396 The SAM domain-containing protein 1 (SAMD1) acts as a repressive chromatin regulator at unmethylated CpG islands
BioSample SAMN13937614
SRA SRX7643919

Supplementary file Size Download File type/resource 155.6 Mb (ftp)(http) BW 151.7 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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