NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4773847 Query DataSets for GSM4773847
Status Public on May 13, 2021
Title RNA-Seq WT2 repl3
Sample type SRA
 
Source name E14TG2a
Organism Mus musculus
Characteristics cell line: E14TG2a
genotype: WT
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 total RNA
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 RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 550
 
Description NormalizedCounts-WT-KDM1AKO-L3MBTL3KO.txt
DeSeq2-KDM1AKOvsWT.txt
DeSeq2-L3MBTL3KOvsWT.txt
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: txt
 
Submission date Sep 09, 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 SAMN16088989
SRA SRX9100293

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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