|
| Status |
Public on Jun 11, 2024 |
| Title |
Mixed Multiplexed_Gene Expression_Lib1 |
| Sample type |
SRA |
| |
|
| Source name |
Hepatocytes, mRNA-derived cDNA
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Hepatocytes
tissue: Liver
strain: BL6
treatment: HDTV
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Livers were harvested and digested using the Miltenyi Biotec Mouse Liver Dissociation kit and individually-labelled with hashtag-oligos according to manufacturer's protocol (Biolegend, TotalSeqTM-B, v3.1 single index). 8000 mVenus-expressing cells from each sample was flow-sorted, and multiplexed for single-cell RNAseq.
Libraries were prepared according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics), the multiplexed cell suspension was loaded onto 2 lanes n the 10x Chromium Genomics platform for single cell encapsulation and library preparation according to the manufacturer’s instructions (10x Genomics Chromium Single Cell 3' GEM v3 workflow). Standard 10x Genomics parameters were used for sequencing: read1: 28bp, index1: 8bp, index2: 0bp, read2: 91bp. The libraries were sequenced on 1 lane of an S1 flowcell on an Illumina NovaSeq 6000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
|
| |
|
| Submission date |
Jan 06, 2023 |
| Last update date |
Jun 11, 2024 |
| Contact name |
Adelyne SL Chan |
| E-mail(s) |
Adelyne.Chan@cruk.cam.ac.uk
|
| Organization name |
University of Cambridge
|
| Department |
Cancer Research UK
|
| Lab |
Narita Lab
|
| Street address |
Li Ka Shing Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0RE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE222338 |
Single cell RNAseq of hepatocytes isolated from UBC-injected mice at different timepoints post-HDTV |
| GSE222951 |
Titration of RAS alters senescent state and influences tumour initiation |
|
| Relations |
| BioSample |
SAMN32618257 |
| SRA |
SRX18955849 |
