|
| Status |
Public on Apr 18, 2023 |
| Title |
NanogKO (44C6) rep2 S4 |
| Sample type |
SRA |
| |
|
| Source name |
N{delta}
|
| Organism |
Mus musculus |
| Characteristics |
cell line: N{delta}
cell type: ESC
genotype: N{delta}
|
| Treatment protocol |
no treatment
|
| Growth protocol |
SL (Serum:Lif) medium: GMEM (Sigma) supplemented with 10% fetal bovine serum (FBS) (Gibco), 100 μM 2-mercaptoethanol (Sigma), 1× MEM non-essential amino acids, 2 mM l-glutamine, 1 mM sodium pyruvate (all from Gibco), 1,000 U ml−1 leukaemia inhibitory factor (LIF) (made in house)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were flow sorted using AriaIII (BD Biosciences, BD Diva Software) cell sorter, for PECAM+PDGFRA- cells.
Total RNA was collected using the RNeasy Mini Kit (Qiagen). Genomic DNA was eliminated by Dnase treatment (Qiagen).
Ribosomal RNA was removed using the NEBNext rRNA depletion kit. Sequencing libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw reads where processed with bcl2fastq (v 2.19.1)
STAR (v 2.5.3a) was used to map sequencing reads and generate the count table (Dobin et al. 2013).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Jul 06, 2022 |
| Last update date |
Apr 18, 2023 |
| Contact name |
Josh M Brickman |
| E-mail(s) |
joshua.brickman@sund.ku.dk
|
| Organization name |
Copenhagen University
|
| Department |
reNEW
|
| Lab |
Brickman
|
| Street address |
3B Blegdamsvej
|
| City |
Copenhagen |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE207560 |
A Bipartate function of ESRRB integrates signaling over time to balance self-renewal and differentiation [RNA-Seq] |
| GSE207565 |
A Bipartate function of ESRRB integrates signaling over time to balance self-renewal and differentiation |
|
| Relations |
| BioSample |
SAMN29532830 |
| SRA |
SRX16037704 |
