|
| Status |
Public on May 19, 2021 |
| Title |
E25 ctr3 |
| Sample type |
SRA |
| |
|
| Source name |
MEF
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Mouse Embryonic Fibroblasts
genotype: Eset1 cKO
|
| 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 |
control
|
| 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 |
| E-mail(s) |
erikson@ie-freiburg.mpg.de
|
| 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 |
|
| Relations |
| BioSample |
SAMN13571603 |
| SRA |
SRX7388172 |
