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Series GSE101099 Query DataSets for GSE101099
Status Public on Aug 13, 2018
Title Lineage dynamics of pancreatic development at single cell resolution
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary A developmental, single-cell transcriptional timecourse analysis was performed on murine pancreas from embryonic days 12, 14, and 17. Whole embryonic murine pancreas tissue was dissociated to single cells, stained with a dead-cell indicator, and subjected to fluorescence activated cell sorting (FACS) to select all live cells.  Single cell RNA-sequencing libraries were then subsequently generated for 4,631 cells at E12, 9,028 cells at E14 (comprised of two independent batches), and 4,635 cells at E17.  Cells were sequenced at a depth of ~60,000 reads/cell (E14 Batch 1) or ~30,000 reads/cell (E12, E14, and E17 Batch 2). Identification of a novel epithelial progenitor population and multiple novel mesenchymal populations showcases the power of single cell RNA-sequencing to uncover previously uncharacterized cell types, and highlights the dynamic cellular heterogeneity of the developing pancreas.
 
Overall design Data set 1: Single cell sequencing of embryonic Swiss Webster murine pancreatic tissue using the HiSeq 2500. Live cells were collected from E12.5, E14.5, and E17.5 whole pancreata and prepared using the 10x Single Cell instrument and v1 10X single cell kits according to standard protocol. The first batch consisted of 1 E14.5 litter and was run on 1 well of the 10X instrument. The second batch consisted of 1 well each of E12.5, E14.5, and E17.5 pancreata.

Data set 2: Single-cell RNA-sequencing was performed on embryonic Swiss Webster or Fev-Cre;ROSA26mTmG murine pancreatic tissue using the NovaSeq. Live cells were collected from E12.5, E14.5, and E17.5 (Swiss Webster) and E14.5 (Fev-Cre;ROSA26mTmG) whole pancreata and prepared using the 10x Single Cell instrument (10X Genomics) and the v2 10X single cell kits according to manufacturer's instructions.
 
Contributor(s) Byrnes LE, Wong DM, Subramaniam M, Meyer NP, Gilchrist CL, Knox SM, Tward AD, Ye CJ, Sneddon JB
Citation(s) 30254276
Submission date Jul 10, 2017
Last update date Mar 21, 2019
Contact name Julie B Sneddon
E-mail(s) Julie.Sneddon@ucsf.edu
Organization name UCSF
Street address 500 Parnassus Ave.
City San Francisco
State/province California
ZIP/Postal code 94122
Country USA
 
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (10)
GSM2699154 E14.5 Batch 1
GSM2699155 E14.5 Batch 2
GSM2699156 E12.5 Batch 2
Relations
BioProject PRJNA393711
SRA SRP111476

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE101099_RAW.tar 496.6 Mb (http)(custom) TAR (of MTX, TSV)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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