NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4287311 Query DataSets for GSM4287311
Status Public on May 13, 2021
Title SAMD1_WT_repl2
Sample type SRA
 
Source name E14TG2a
Organism Mus musculus
Characteristics antibody: SAMD1 (self-made)
genotype: WT
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 or mm10 using Bowtie 1.0, allowing one mismatch.
SAM files were converted to bigwig files using SamTools, and deepTools/bamCoverage. Data were normalized to RPKM.
RNA-Seq data were aligned to mouse transcriptome GenCode.M23 using RNA Star. Counts per gene were determined using FeatureCounts . Differentially expressed genes and normalized reads were determined using DeSeq2.
Genome_build: mm9, mm10
Supplementary_files_format_and_content: bw
 
Submission date Jan 28, 2020
Last update date May 13, 2021
Contact name Robert Liefke
E-mail(s) robert.liefke@imt.uni-marburg.de
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
Relations
BioSample SAMN13937629
SRA SRX7643904

Supplementary file Size Download File type/resource
GSM4287311_SAMD1-WT-repl2-mm10.bw 134.4 Mb (ftp)(http) BW
GSM4287311_SAMD1-WT-repl2-mm9.bw 122.3 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap