|
| Status |
Public on Dec 04, 2020 |
| Title |
5ar2.23 |
| Sample type |
SRA |
| |
|
| Source name |
Formative pluripotent stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: 5ar2
cell type: Pluripotent stem cells
condition: Formative
|
| Treatment protocol |
N/A
|
| Growth protocol |
FS cells were cultured in A3XR, AF cells were cultured in AF and AFX cells were cultured in AFX.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were directly sorted into each well of 96-well plate filled with 2.3 µl of lysis buffer (1 unit/µl of SUPERaseIN RNase inhibitor (Invitrogen), 0.2% Triton X) by BD FACSAria Fusion (BD Biosciences).
Libraries were prepared by Smart-seq2 (Illumina) followed by previously described (Picelli et al., 2014).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Sample 119
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv
|
| Data processing |
The quality of the data was assessed using FastQC and MultiQC.
The reads were aligned using STAR v2.7.3a (parameters --outSAMtype BAM SortedByCoordinate).
Protein-coding gene quantification was performed using Subread featureCounts v2.0.0 (default parameters), only uniquely mapped reads were used.
Cells with fewer than 3m reads total were discarded from further analysis.
Raw expression levels were normalized with sctransform.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: raw.csv contains raw gene counts.
Supplementary_files_format_and_content: normalized.csv contains cells sctransform-normalized expression levels of cells that passed QC.
|
| |
|
| Submission date |
Aug 20, 2020 |
| Last update date |
Dec 04, 2020 |
| Contact name |
Irina Mohorianu |
| E-mail(s) |
data-submissions@stemcells.cam.ac.uk
|
| Organization name |
University of Cambridge
|
| Department |
Wellcome-MRC Cambridge Stem Cell Institute
|
| Street address |
Puddicombe Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0AW |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE156588 |
Capture of mouse and human stem cells with features of formative pluripotency [scRNA-seq] |
| GSE156589 |
Capture of mouse and human stem cells with features of formative pluripotency |
|
| Relations |
| BioSample |
SAMN15869347 |
| SRA |
SRX8980007 |
