|
| Status |
Public on Aug 10, 2023 |
| Title |
spindrop mouse nascent RNA 5EU-seq sample 2 |
| Sample type |
SRA |
| |
|
| Source name |
Embryos at E8.5 whole embryo
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Embryos at E8.5 whole embryo
cell line: CD-1
cell type: embryos
treatment: Sample was dissected and cultured for 3 hours in IVC1 with the 5EU analog, cells were then dissociated with TrypLE Express for 15 minutes at 37C, Click-chemistry was performed as per the scEU-seq protocol and cells were processed using spindrop without sorting. After de-emulsification and clean-up the "nascent" samples are eliuted from the streptavidin beads before downstream library preparation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Live cells were stained with PE-labelled antibodies or Calcein-AM
Bead barcoding: indrop v3 protocol, encapsulation: spinDrop protocol, downstream library preparation: inDrop v3 protocol
inDrop v3 protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
nascent RNA
spinDrop 5EU-seq
EU_E85_nascent_matrix.csv
|
| 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.
|
| |
|
| Submission date |
Aug 07, 2023 |
| Last update date |
Aug 10, 2023 |
| 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) |
| GSE208156 |
spinDrop: a modular droplet microfluidic platform to maximise single-cell RNA sequencing information content |
|
| Relations |
| BioSample |
SAMN36871500 |
| SRA |
SRX21278075 |
