GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM3140915 Query DataSets for GSM3140915
Status Public on Aug 13, 2018
Title E12.5 SW
Sample type SRA
Source name pancreatic cells
Organism Mus musculus
Characteristics strain: Swiss Webster
tissue: pancreas
developmental stage: E12.5
Extracted molecule total RNA
Extraction protocol Pancreata were isolated from mouse embryos and dissociated in TrypLE Express at 37C with pipet trituration at 5-minute intervals during incubation. E12.5 pancreata were dissociated for 10 minutes, E14.5 pancreata for 15 minutes, and E17.5 pancreata for 30 minutes. Dissociations were neutralized with FACS buffer (10% FBS + 2mM EDTA in phenol-red free HBSS). Dissociated cells were passed through a 30um cell strainer and stained with Sytox live/dead stain (Thermo Fisher), along with protocol specific stains noted in the individual sample extract protocol descriptions. Stained cells were washed twice in FACS buffer and then processed through a BD FACS Aria II.
For Swiss Webster embryonic pancreatic dissociations, cells were also stained with the mesenchymal marker, CD140a. Stained cells were washed twice in FACS buffer and then processed through a BD FACS Aria II. To enrich for epithelial populations, live, CD140a- cells were collected from E12.5, E14.5, and E17.5 Swiss Webster pancreata.
cDNA libraries were prepared for sequencing using standard protocol for the 10x Single Cell instrument with v2 kit and reagents.
droplet-based single cell RNA-Seq
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description single cell RNA sequencing of E12.5 swiss webster pancreas
Read 1= 98, Index read 1 (i7)= 14, Index read 2 (i5)= 8, Read 2= 10
Data processing Data were processed according to the 10x Cellranger pipeline.
BAM files were generated with v2.1 10X Genomics Cellranger software using default parameters.
Gene-barcode matrices were generated from Cellranger v2.1 using default parameteres.
Genome_build: mm10 for all Swiss Webster. For Fev-Cre;Rosa26mTmG, eGFP and TdTomato sequences from the mTmG mouse line (Muzumdar MD. et. al., 2007) were added to the mm10 genome FASTA and annotations. The genome was prepared as according to 10X Genomics instructions for custom genome builds.
Supplementary_files_format_and_content: Cellranger outputs a .mtx file with the gene-barcode matrix. This matrix contains the counts of molecules per cell (UMI/cell) as determined after filtering and counting by Cellranger. The matrix is in market exchange format while the row (gene names) and columns (cell barcodes) are provided as TSV files. File formats are documented in Cellranger software manual.
Submission date May 14, 2018
Last update date Aug 14, 2018
Contact name Jeremy Reiter
Organization name UCSF
Street address 555 Mission Bay Boulevard South
City San Francisco
State/province California
ZIP/Postal code 94158
Country USA
Platform ID GPL24247
Series (1)
GSE101099 Lineage dynamics of pancreatic development at single cell resolution
BioSample SAMN09205831
SRA SRX4080245

Supplementary file Size Download File type/resource
GSM3140915_E12_v2.mtx.gz 105.6 Mb (ftp)(http) MTX
GSM3140915_E12_v2_barcodes.tsv.gz 50.0 Kb (ftp)(http) TSV
GSM3140915_E12_v2_genes.tsv.gz 212.7 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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