NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6921241 Query DataSets for GSM6921241
Status Public on Jun 11, 2024
Title Mixed Multiplexed_Gene Expression_Lib2
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 SAMN32618256
SRA SRX18955850

Supplementary file Size Download File type/resource
GSM6921241_Lib2_GeneExpression_barcodes.tsv.gz 16.4 Kb (ftp)(http) TSV
GSM6921241_Lib2_GeneExpression_features.tsv.gz 284.1 Kb (ftp)(http) TSV
GSM6921241_Lib2_GeneExpression_matrix.mtx.gz 22.7 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap