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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 02, 2023 |
| Title |
spindrop mES HEK293T species mixing |
| Sample type |
SRA |
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| Source name |
kidney, Embryo
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| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
tissue: kidney, Embryo
cell line: HEK293T, mESC
cell type: cultured cells
genotype: WT/WT
treatment: HEK293T cultured in DMEM supplemented with 10% FBS, mESC cells cultured in 2i/LIF. HEK293T were dissociated with Trypsin-EDTA for 5 minutes at 37C , mESCs were dissociated with Accutase. Cells were pooled at equal concentrations and stained with Calcein-AM before being processed using spinDrop.
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| Extracted molecule |
total RNA |
| Extraction protocol |
HEK293T cultured in DMEM supplemented with 10% FBS, mESC cells cultured in 2i/LIF. HEK293T were dissociated with Trypsin-EDTA for 5 minutes at 37C , mESCs were dissociated with Accutase. Mouse brain dissections were dissociated with with TrypLE Express for 15 minutes at 37C. For nuclei preparations the Nuclei EZ prep kit. For the paraformaldehyde (PFA) treatment, 4% PFA was used. Live celsl were stained with Calcein-AM, PFA-fixed cells and nuclei were stained with Vybrant green.
Bead barcoding: indrop v3 protocol, encapsulation: spinDrop protocol, downstream library preparation: inDrop v3 protocol
inDrop v3 protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
spindrop
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| Data processing |
FastQC quality control
Pheniqs for demultiplexing
zUMIs to generate gene expression matrices using mouse and human references with Ensembl v99 annotations
Seurat v3 for data integration and analysis
Assembly: GRCm38 genome (Ensembl 99) and GRCh38 genome (Ensembl 99)
Supplementary files format and content: UMI quantified reads mapping to intronic and exonic regions. Downsampled to 20,000 reads per cell when indicated in the file header.
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| Submission date |
Jul 13, 2022 |
| Last update date |
Jul 02, 2023 |
| Contact name |
Florian Hollfelder |
| E-mail(s) |
fh111@cam.ac.uk
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| Organization name |
University of Cambridge
|
| Street address |
80 tennis court road
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| City |
Cambridge |
| ZIP/Postal code |
CB21GA |
| Country |
United Kingdom |
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| Platform ID |
GPL19415 |
| Series (1) |
| GSE208156 |
spinDrop: a modular droplet microfluidic platform to maximise single-cell RNA sequencing information content |
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| Relations |
| BioSample |
SAMN29720338 |
| SRA |
SRX16207130 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6338233_spindrop_species_mixing_whole_cell_hg19.inex.txt.gz |
1.6 Mb |
(ftp)(http) |
TXT |
| GSM6338233_spindrop_species_mixing_whole_cell_mm10.inex.txt.gz |
960.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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