|
| Status |
Public on Nov 30, 2019 |
| Title |
SB-EP, SB-2ilif and NatE45 (mixture of 6 samples) |
| Sample type |
SRA |
| |
|
| Source name |
Cells extracted from the synthetic blastocyst (SB) built with extended pluripotent stem cells and trophoblast stem cells. Cells extracted from the synthetic blastocyst (SB) built with conventional embryonic stem cells and trophoblast stem cells.
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mixed sample (non-demultiplexed) representing SB-EP, SB-2iLif and NatE45 cells
|
| Treatment protocol |
no treatment was used.
|
| Growth protocol |
Cell suspension seeded in aggregation plates. Grown in sequencial media.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Blastoids (n=100 per group) were exposed to Tryple Express Select X10 (Thermofisher A1217701) for 15 mins in 37°C, and subsequently dissected with glass capillaries of different diameters. For ESC-derived blastoid group; total of 1,154 cells including 752 ESCs, 350 TSCs 52 PE-like cells extracted. For EPSCderived blastoid group; total of 2,350 cells including 1,087 EPSC, 1,140 TSCs 123 PE-like cells extracted.
Indrop v3
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
6 mixed samples: SB-EP1, SB-EP2, SB-EP3, SB-2ilif1, SB-2ilif2, NatE45
|
| Data processing |
R1 is the biological read.
R2 carries the first half of the gel barcode.
R3 carries the library index.
R4 the second half of the gel barcode (8 cycles) and the UMI (6 cycles).
indropv3 filtering and demultiplexing
indropv3 identify abundant barcodes
indropv3 quantify expression
indropv3 sort
indropv3 aggregate
scrublet remove doublets
Genome_build: Mus_musculus.GRCm38.dna_sm.primary_assembly.fa
Supplementary_files_format_and_content: indrop quantification matrices converted to 10x format
|
| |
|
| Submission date |
Jul 13, 2019 |
| Last update date |
Dec 01, 2019 |
| Contact name |
Florian Hollfelder |
| E-mail(s) |
fh111@cam.ac.uk
|
| Organization name |
University of Cambridge
|
| Street address |
80 tennis court road
|
| City |
Cambridge |
| ZIP/Postal code |
CB21GA |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE134240 |
Single Cell RNA-seq analysis of gene expression patterns of cells from stem-cell-derived-synthetic-blastocysts, called as 'ES-' or 'EPS-blastoids'. |
|
| Relations |
| BioSample |
SAMN12268041 |
| SRA |
SRX6438795 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3940220_NatE45_.mtx.gz |
965.8 Kb |
(ftp)(http) |
MTX |
| GSM3940220_NatE45_.tsv.gz |
668 b |
(ftp)(http) |
TSV |
| GSM3940220_NatE45_genes.tsv.gz |
180.7 Kb |
(ftp)(http) |
TSV |
| GSM3940220_SB-EP_1_barcodes.tsv.gz |
6.9 Kb |
(ftp)(http) |
TSV |
| GSM3940220_SB-EP_1_genes.tsv.gz |
180.7 Kb |
(ftp)(http) |
TSV |
| GSM3940220_SB-EP_1_matrix.mtx.gz |
6.4 Mb |
(ftp)(http) |
MTX |
| GSM3940220_SB-EP_2_barcodes.tsv.gz |
5.0 Kb |
(ftp)(http) |
TSV |
| GSM3940220_SB-EP_2_genes.tsv.gz |
180.7 Kb |
(ftp)(http) |
TSV |
| GSM3940220_SB-EP_2_matrix.mtx.gz |
5.9 Mb |
(ftp)(http) |
MTX |
| GSM3940220_SB-EP_3_barcodes.tsv.gz |
6.8 Kb |
(ftp)(http) |
TSV |
| GSM3940220_SB-EP_3_genes.tsv.gz |
180.7 Kb |
(ftp)(http) |
TSV |
| GSM3940220_SB-EP_3_matrix.mtx.gz |
7.1 Mb |
(ftp)(http) |
MTX |
| GSM3940220_SB2ilif1_barcodes.tsv.gz |
5.3 Kb |
(ftp)(http) |
TSV |
| GSM3940220_SB2ilif1_genes.tsv.gz |
180.7 Kb |
(ftp)(http) |
TSV |
| GSM3940220_SB2ilif1_matrix.mtx.gz |
4.8 Mb |
(ftp)(http) |
MTX |
| GSM3940220_SB2ilif2_barcodes.tsv.gz |
3.3 Kb |
(ftp)(http) |
TSV |
| GSM3940220_SB2ilif2_genes.tsv.gz |
180.7 Kb |
(ftp)(http) |
TSV |
| GSM3940220_SB2ilif2_matrix.mtx.gz |
3.3 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
