|
| Status |
Public on Sep 25, 2017 |
| Title |
TET2rescue-Mut-2i-2 |
| Sample type |
SRA |
| |
|
| Source name |
embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: Tet2 KO
medium: 2i
shRNA: shSetdb1
rescue: TET2 Mut
|
| Treatment protocol |
Lentiviral particles containing pLKO.1 shRNA vectors were produced by standard methods in 293T cells. Transduced ES cells were selected with 1 µg/ml puromycin 48 hours post-infection and collected after 3 days of selection.
|
| Growth protocol |
ESCs were cultured on gelatin-coated plates without feeders, in either: 1) serum media (DMEM supplemented with 15% fetal bovine serum and 1,000 U/ml LIF), or 2) 2i media (DMEM F-12 and neurobasal media supplemented with N2, B27, LIF, PD0325901 and CHIR99021).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using either the AllPrep DNA/RNA mini kit (QIAGEN) and DNAse treated with the TURBO DNA-free kit (Ambion).
Non-directional mRNA-Seq libraries were generated using the Dynabeads mRNA purification kit (Life Technologies) and the NEBnext Ultra RNA library prep kit (NEB).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Adaptors and low-quality base calls were trimmed using trim_galore! v0.3.3 with default parameters.
Trimmed reads were mapped to mm9 using tophat v2.0.9 with -g 1.
Raw read counts for each gene or repeat (from RepeatMasker annotation) were generated in Seqmonk with the RNA-seq quantitation pipeline. Reads from repeats belonging to the same class were pooled. Normalised gene and repeat expression values were calculated with the variance stabilizing transformation in DESeq2.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files containing normalised gene expression values (log2) for each sample.
|
| |
|
| Submission date |
Jul 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Miguel R Branco |
| E-mail(s) |
m.branco@qmul.ac.uk
|
| Organization name |
Blizard Institute
|
| Street address |
4 Newark Street
|
| City |
London |
| ZIP/Postal code |
E1 2AT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE100863 |
Rescue of Tet2 KO ES cells in primed or naïve state |
| GSE100864 |
SETDB1 prevents TET2-dependent activation of IAP retroelements in naïve embryonic stem cells |
|
| Relations |
| BioSample |
SAMN07327533 |
| SRA |
SRX2987257 |
