|
| Status |
Public on Oct 28, 2022 |
| Title |
Ctrl mESCs after tamoxifen treatment, rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Control mESCs
|
| Organism |
Mus musculus |
| Characteristics |
strain: CreERT2 wt/ki; Gt(ROSA)26Sor<tm1Ytchn>/Jwt/ki and CreERT2 wt/ki; Gt(ROSA)26Sor<tm1Ytchn>/Jwt/ki
cell type: mESCs
age: 6.5 days after tamoxifen-treatment
treatment: tamoxifen (1µM) treatment for 2.5 days then 4 additional days in culture
genotype: control
|
| Treatment protocol |
mESCs were treated with tamoxifen (1µM) for 2.5 days and then cultured for 4 additional days.
|
| Growth protocol |
mESC were cultured under 2i-conditions (CHIR99021 and PD0325901) using Mouse Embryonic Fibroblasts (MEFs) as feeders.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
CD326+/GFP+/Live/Thy1.2-/LiveDead dye- mESCs were sorted from Tamoxifen-treated mESCs (either Ctrl or TetiTKO). And total RNA were extracted using Qiagen RNeasy plus micro kit
Libraries were constructed using the Smart2seq protocol.
50x50bp pair end sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Paired reads were mapped with STAR using the parameters (--outFilterMultimapNmax 1 --outSAMattributes All --outSAMprimaryFlag OneBestScore –sjdbOverhang 100 --outSAMtype BAM SortedByCoordinate).
Counts per gene were obtained from htseq-count (version 0.7.1.); Differential Gene Expression was done with R (version 3.5.2) using the DESEQ2 package (version 1.26.0).
A gene was considered DGE if both the absolute Log2FC was ≥ 0.5 and a adj.pvalue (FDR) ≤0.05 threshold was met.
Genome_build: Mus Musculus genome (version mm9)
Supplementary_files_format_and_content: Tab-Separated Files with Normalized expression per sample.
|
| |
|
| Submission date |
Dec 16, 2021 |
| Last update date |
Oct 28, 2022 |
| Contact name |
Hugo Sepulveda |
| E-mail(s) |
[email protected]
|
| Organization name |
La Jolla Institute for Immunology
|
| Department |
Division of Signaling and Gene Expression
|
| Lab |
Anjana Rao
|
| Street address |
9420 Athena Circle
|
| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE191045 |
Acute deletion of TET enzymes results in aneuploidy in mouse embryonic stem cells through decreased expression of Khdc3 |
|
| Relations |
| BioSample |
SAMN24116432 |
| SRA |
SRX13426779 |
