|
| Status |
Public on Mar 06, 2019 |
| Title |
HUB-JF-03 (scRNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
pTS1 pTSCs isolated from blastoids
|
| Organism |
Mus musculus |
| Characteristics |
genetic background: C57BL/6J
date sorting: 20180413
cell type: pTS1 pTSCs isolated from blastoids
genotype: include randomly integrated GFP expression cassete
|
| Growth protocol |
TSCs grown in Tx conditions (Kubaczka, 2014)
[pTSC growth protocol] TSCs grown in Lt21 conditions (Kubaczka, 2014)
[differentiation protocol ] TSC plate din Tx conditions. 24 hours media is refreshed with fresh Tx without growth factors.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were sorted into 384 well plates. All wells underwent Cel-Seq2 protocol
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
single cell library
|
| Data processing |
Sequencing libraries were mapped with STAR-2.5.3a with default parameters to the ensembl version 93 of the mouse genome, and only reads mapping to gene bodies (exons or introns) were used for downstream analysis. Reads mapping simultaneously to an exon and to an intron were assigned to the exon.
Ensembl version 93 of the mouse genome
Tabular-separated file indicating number of transcripts per section obtained as previously described (Grün, Dominic, Lennart Kester, and Alexander Van Oudenaarden. "Validation of noise models for single-cell transcriptomics." Nature methods 11.6 (2014): 637). We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads, *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI-corrected transcripts per gene per cell
|
| |
|
| Submission date |
Mar 03, 2019 |
| Last update date |
Mar 09, 2019 |
| Contact name |
Nicolas Rivron |
| Phone |
+31302121800
|
| Organization name |
Hubrecht Institute / Maastricht University
|
| Lab |
Rivron
|
| Street address |
Uppsalalaan 8
|
| City |
Utrecht |
| State/province |
Utrecht |
| ZIP/Postal code |
3584CT |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE127754 |
Single cell transcriptome analysis of TSCs differentiated TSCs, pTSCs and pTSCs isolated from blastoid |
|
| Relations |
| BioSample |
SAMN11045937 |
| SRA |
SRX5457673 |
