|
| Status |
Public on Jun 17, 2021 |
| Title |
ESC O4f/- CreER 0h RNA rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: Mixed 129SV C57BL/6
cell type: Embryonic stem cells
treatment: Untreated
genotype: Oct4Fl/-; CAG CreER
|
| Treatment protocol |
Cells were treated with 500nM 4OHTor 500μM IAA as described.
|
| Growth protocol |
Cells were grown in N2B27 supplemented with 1μM PD03, 3μM Chiron and 1x mLIF, passaged as required using accutase onto tissue-culture plastic precoated in 0.1% gelatin in PBS. ZHBT ESCs were maintained with 1μg/ml doxycylin to prevent expression of wild-type Oct4.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using a Qiagen Rneasy mini kit with on-column DNA digest.
Depletion of ribosomal RNA was performed on 2-5 μg of total RNA using the Ribo-Zero rRNA Removal Kitand libraries were produced from 10-100ng of ribosomal-depleted RNA using NextFlex Rapid Directional RNA-seq Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Adapters were trimmed and low quality sequences removed using TrimGalore v0.1.4, then aligned to mm10 using TopHat2 v2.1.0 with parameters --read-mismatch 1 --max-multihits 1
Gene-wise counts were generated using featureCounts v1.5.1 based on annotation from Ensembl GRCm38.86 release.
Normalization was performed using NOISeq: low count genes were excluded using CPM filtering with a cutoff of 1 CPM before TMM normalization was performed.
Genome_build: mm10
Supplementary_files_format_and_content: csv files containing raw gene counts for each sample
Supplementary_files_format_and_content: csv file containing TMM normalized counts for each gene for all samples
|
| |
|
| Submission date |
Mar 09, 2021 |
| Last update date |
Jun 16, 2023 |
| Contact name |
Lawrence E Bates |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Edinburgh
|
| Department |
Human Genetics Unit
|
| Lab |
Nichols Lab
|
| Street address |
Crewe Road
|
| City |
Edinburgh |
| ZIP/Postal code |
EH4 2XU |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE168577 |
Auxin-degron system identifies immediate mechanisms of Oct4 [RNA-seq] |
| GSE168579 |
Auxin-degron system identifies immediate mechanisms of Oct4 |
|
| Relations |
| BioSample |
SAMN18235573 |
| SRA |
SRX10297666 |
