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Sample GSM2699157 Query DataSets for GSM2699157
Status Public on Aug 13, 2018
Title E17.5 Batch 2
Sample type SRA
 
Source name pancreatic cells
Organism Mus musculus
Characteristics strain: Swiss Webster
tissue: pancreas
developmental stage: E17.5
Extracted molecule total RNA
Extraction protocol Pancreata were isolated from Swiss Webster 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). Stained cells were washed twice in FACS buffer and then processed through a BD FACS Aria II; all live cells were collected.
cDNA libraries were prepared for sequencing using standard protocol for the 10x Single Cell instrument; droplet-based single cell RNA-Seq
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description single cell RNA sequencing of E17.5 pancreas (batch 2)
read length: 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 v1.1 10X Genomics Cellranger software using default parameters.
Gene-barcode matrices were generated from Cellranger v1.1 using default parameteres.
Genome_build: mm10
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 Jul 10, 2017
Last update date Aug 14, 2018
Contact name Jeremy Reiter
E-mail(s) jeremy.reiter@ucsf.edu
Organization name UCSF
Street address 555 Mission Bay Boulevard South
City San Francisco
State/province California
ZIP/Postal code 94158
Country USA
 
Platform ID GPL17021
Series (1)
GSE101099 Lineage dynamics of pancreatic development at single cell resolution
Relations
BioSample SAMN07339974
SRA SRX2994145

Supplementary file Size Download File type/resource
GSM2699157_E17_B2.mtx.gz 10.0 Mb (ftp)(http) MTX
GSM2699157_E17_B2_barcodes.tsv.gz 17.9 Kb (ftp)(http) TSV
GSM2699157_E17_B2_genes.tsv.gz 211.0 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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