|
| Status |
Public on Jun 16, 2022 |
| Title |
XEGs replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Cell culture
|
| Organism |
Mus musculus |
| Characteristics |
starting cells: mouse ES cells, XEN cells
|
| Treatment protocol |
No treatment
|
| Growth protocol |
Growth protocol P3 with chiron as described in van den Brink et al (2014) in Development. Differences: Gastruloids start with 200 E14 mouse embryonic stem cells (mESCs), PEGs start with a mixture 150 E14 mESCs and 50 Extra-embryonic-endoderm-like (XEN) cells and cells are collected after 4 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Organoids were pooled and disociated with TrypLE. Spike-ins (see sample descriptions) were added before proceeding with single-cell RNA sequencing library preparation.
10X library: 10x RNA-seq libraries were prepared using the Chromium Single Cell 3' Reagent Kit, Version 3 Chemistry (10x Genomics) according to the manufacturer's protocol. CITE-seq libraries: CITE-seq libraries were prepared according to the CITE-seq protocol from New York Genome Center version 2019-02-13. Sequencing: Libraries were sequenced on an Illumina Novaseq6000 at 150bp paired end.
Paired end RNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Contains E14 mESC CITE-seq spike-ins (CD15 antibody)
|
| Data processing |
Single-cell expression was quantified using unique molecular identifiers (UMIs) by 10x Genomics’ “Cell Ranger” software.
Counts were normalized with the scran package in R
Cell types were assigned by vote of the K-nearest-neighbors from the Pijuan-Sala dataset (GSE87038)
Genome_build: mm10 with mCherry and eGFP
CITE in the name indicates CITE-seq library preparation
Supplementary_files_format_and_content: fq.gz: compressed raw fastq file from illumina sequencing (CITE in the name indicates CITE-seq library preparation); matrix.mtx.gz:compressed matrix of UMI counts where cells are columns and genes rows; barcodes.tsv: compressed list of 16bp barcodes corresponding to the columns of matrix; features.fq.gz: compressed list of HUGO and ensembl identifiers corresponding to the rows of matrix; normCounts.tsv: Compressed table of normalized expression and cell type assignments.
|
| |
|
| Submission date |
Dec 05, 2019 |
| Last update date |
Jun 16, 2022 |
| Contact name |
Stefan Semrau |
| E-mail(s) |
semrau@physics.leidenuniv.nl
|
| Phone |
0031638304530
|
| Organization name |
Leiden University
|
| Department |
Physics
|
| Street address |
Einsteinweg 55
|
| City |
Leiden |
| State/province |
Zuid-Holland |
| ZIP/Postal code |
2333CC |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE141530 |
A gastruloid model of the interaction between embryonic and extra-embryonic cell types |
|
| Relations |
| BioSample |
SAMN13491085 |
| SRA |
SRX7276938 |
