|
| Status |
Public on Aug 21, 2023 |
| Title |
Human Naive Stem Cells, BAP(J) medium, maintained for 3 days |
| Sample type |
SRA |
| |
|
| Source name |
WIBR3
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: WIBR3
cell type: Trophoectoderm
genotype: WT
treatment: BAP(J) (3 days)
|
| Treatment protocol |
24 hours before the induction, cells were plated in HENSM on 1% Matrigel (corning 356231) -coated plates supplemented with 10 µM ROCKi Y27632 (Axon 1683), next day the protocol was started. The 3-day protocol for human TE induction/priming: : BAP(J) media was used for 72 hours. This medium consisted on 2 µM TGFRi A83-01 and 2 µM MEKi/ERKi PD0325901 base, which was complemented the first 24h with 10ng/ml Human recombinant BMP4 (Peprotech) and then substituted with for 1µM JAK inhibitor I (Calbiochem 420099) on day 2 and 3. Please see paper's Methods for further details
|
| Growth protocol |
Human naïve pluripotent stem-cells were expanded in human HENSM conditions for at least 3 passages.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA extracted according to 10x Genomics Chromium v3.1 Dual Index system kit instructions
10x Genomics Chromium v3.1 Dual Index system (5000 cell target cell recovery)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
WT WIBR3 human naïve stem-cells, maintained in BAP(J) medium for 3 days, to induce Trophoectoderm lineage
filtered_feature_bc_matrix.tgz
|
| Data processing |
Demultiplexing was done with bcl2fastq2
Alignment and quantification of single cell features was done with cellranger/7.1.0 counts
Aggregation of the two samples was done using cellranger aggr
Cells with under 1000 expressing genes, over 8000 expressing genes or over 15% mitochondrial gene expression were filtered out for the rest of the analysis.
Seurat integrated analysis and anchoring of 2 individual samples was performed and then normalized by log-normalization using a scale-factor of 10,000. The top 2,000 variable genes were identified by the variance stabilizing transformation method, and subsequently scaled and centered.
Assembly: hg38
Supplementary files format and content: filtered_feature_bc_matrix.tgz includes CellRanger output files that were used in the analysis process. The order of the samples in filtered_feature_bc_matrix.tgz is: 1 - Human Naive Stem Cells, RCL medium, maintained for 3 days, 2 - Human Naive Stem Cells, BAP(J) medium, maintained for 3 days.
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| |
|
| Submission date |
Aug 21, 2023 |
| Last update date |
Aug 22, 2023 |
| Contact name |
Noa Novershtern |
| E-mail(s) |
noa.novershtern@weizmann.ac.il
|
| Organization name |
Weizmann Institute of Science
|
| Department |
Molecular Genetics
|
| Street address |
Weizmann Institute
|
| City |
Rehovot |
| ZIP/Postal code |
7610001 |
| Country |
Israel |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE239932 |
A Human Post-Implantation Embryoid Model Derived Ex Utero Solely from Genetically Unmodified Naïve PSCs |
| GSE241348 |
A Human Post-Implantation Embryoid Model Derived Ex Utero Solely from Genetically Unmodified Naïve PSCs (scRNA-Seq II) |
|
| Relations |
| BioSample |
SAMN37096567 |
| SRA |
SRX21437635 |
