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Sample GSM4220865 Query DataSets for GSM4220865
Status Public on May 19, 2021
Title B1A6 oht3
Sample type SRA
Source name MEF
Organism Mus musculus
Characteristics tissue: Mouse Embryonic Fibroblasts
genotype: Eset1/Eset2/Suv39h1/Suv39h2/G9a/Glp KO
Treatment protocol 4-OHT (1 uM) in culture medium
Growth protocol The growth protocols have been described in our study (Montavon et al). MEFs are grown in standard medium, in presence or absence of 4-hydroxytamoxifen (4-OHT)
Extracted molecule total RNA
Extraction protocol RNA was extracted with trizol and ethanol precipitation, Dnase treated and column-purified
RNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
Description Eset1/Eset2/Suv39h1/Suv39h2/G9a/Glp KO
Data processing Unprocessed reads were first quality and adapter trimmed using cutadapt (Martin M., 2011) version 1.8.1 using a quality threshold of 20. Reads were then aligned to the GRCm38 genome from Ensembl using STAR (Dobin et al., 2013) version 2.5.2b, with settings as recommended by TEtranscripts (Jin Y. et al., 2015). 
Genome_build: GRCm38
Supplementary_files_format_and_content: raw counts in .tsv file
Submission date Dec 16, 2019
Last update date May 19, 2021
Contact name Galina Erikson
Phone +49 (0)761 5108-0
Organization name Max Planck Institute of Immunobiology and Epigenetics
Street address Stübeweg 51
City Freiburg im Breisgau
ZIP/Postal code 79108
Country Germany
Platform ID GPL21493
Series (2)
GSE142103 Complete loss of H3K9 methylation dissolves mouse heterochromatin organization [RNA-seq]
GSE142105 Complete loss of H3K9 methylation dissolves mouse heterochromatin organization
BioSample SAMN13571609
SRA SRX7388190

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

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