|
| Status |
Public on Apr 22, 2023 |
| Title |
pKO1_scRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
mESCs
|
| Organism |
Mus musculus |
| Characteristics |
cell line: R1
genotype/perturbation: promoter KO
|
| Growth protocol |
mESCs were routinely grown on gelatin-coated plates on MEFs in serum-based medium: DMEM (Gibco) containing 15% ES-grade fetal calf serum (Biological Industries), 1X Sodium pyruvate (Gibco), 1X Nonessential amino acids (Gibco), 0.1mM β-mercaptoethanol (Sigma), 100U/ml Penicillin and 0.1 mg/ml Streptomycin (Biological Industries), and 10ng/ml LIF (Weizmann Proteomics Unit). Cells were passaged with 0.25% Trypsin (Biological Industries) every 2–3 days.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were sorted into 384-well plates containing 2nM barcodes and lysis buffer.
MARS-seq barcoding and library preparation were carried out as previously described(Jaitin et al., 2014).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Initial analysis was carried out as described in(Jaitin et al., 2014; Keren-Shaul et al., 2019).
Metacells were constructed and analyzed using the MetaCell package(Baran et al., 2019).
Assembly: mm9
Supplementary files format and content: RNA counts per cell
|
| |
|
| Submission date |
Jan 22, 2023 |
| Last update date |
Apr 22, 2023 |
| Contact name |
Igor Ulitsky |
| E-mail(s) |
igor.ulitsky@weizmann.ac.il
|
| Organization name |
Weizmann Institute of Science
|
| Street address |
Hertzl St.
|
| City |
Rehovot |
| ZIP/Postal code |
76100 |
| Country |
Israel |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE223452 |
Complex regulation of Eomes levels mediated through distinct functional features of the Meteor long non-coding RNA locus (scRNA-Seq) |
| GSE223453 |
Complex regulation of Eomes levels mediated through distinct functional features of the Meteor long non-coding RNA locus |
|
| Relations |
| BioSample |
SAMN32868346 |
| SRA |
SRX19136077 |
