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Sample GSM4191339 Query DataSets for GSM4191339
Status Public on Nov 12, 2020
Title 161088C_C-3
Sample type SRA
 
Source name Dorsal skin epidermis
Organism Mus musculus
Characteristics tissue: Control dorsal skin
age: Newborn mouse
Treatment protocol N/A. Primary cells were used in this study.
Growth protocol N/A. Primary cells were used in this study.
Extracted molecule total RNA
Extraction protocol Human: Human EMPD (Patient ID; n=1) and normal skin (Patient ID; n=1; normal skin constitutes site adjacent to EMPD lesion). Samples were surgically excised and placed in tissue storage solution (MACS). Samples were processed for single cell isolation within 10 hours post-surgery. Excess subcutaneous adipose and dermal tissues were excised. Samples were cut into pieces with a maximum diameter of 4 mm. Skin specimens were then washed twice with cold 1X PBS. Single cells were isolated using the human epidermis isolation kit (MACS) as per manufacturer’s instructions with minor modifications. Mouse: Skin epidermal cells were collected from DTG (n=1) and control (n=1) newborn mice (post-natal day 0.5) 5 days after Doxycycline treatment. Mice were euthanized, and consecutively immersed in 70% ethanol and cold 1X PBS twice for 3 minutes. Fore and hind limbs and tail were cut off and skin was peeled along the ventral midline axis with blunt tweezers. Subcutaneous adipose tissue was micro-dissected. 12 mm skin biopsies were laid on EpiLife CF basal media (STEM CELL) droplets (300 μL) on a 12-well plate with skin dermis side down. 2 ml (2.5 U/mL) Dispase solution (STEM CELL) was added to skin and incubated at 4℃ for 12 hrs. Epidermis was separated from dermis with two sharp tweezers and placed on Accutase (ThermoFisher) droplets (500 μL) for 30 min (dermis side down) at RT to create single cell suspensions.
Single cells were captured using the Chromium Platform (10X Genomics) and libraries were generated using Single Cell 3’ v2 chemistry (mouse samples) and Single Cell 3' v3 chemistry (human samples). Cell capture, library preparation, quality control, and sequencing was performed at Beijing CapitalBio Technology (Beijing, China).
Single Cell 3’ v2 chemistry (mouse samples) - 10X Genomics
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description mRNA from single cells
Data processing Transcripts from human donors were mapped to the reference genome (GRCh38) using Cell Ranger Version 3.0.2
Transcripts from mice were mapped to the reference genome (GRCm38/mm10) using Cell Ranger Version 2.0.1
Quality control of all data sets was performed using Seurat (Version 3.0.0)
Processed files were analyzed with Seurat V3.1.0, Monocle V2.10.1, scEpath V1 and Velocyto.R V0.6.
Genome_build: mm10
Genome_build: GRCh38
Supplementary_files_format_and_content: Cell Ranger output
 
Submission date Nov 25, 2019
Last update date Nov 12, 2020
Contact name Maksim V Plikus
E-mail(s) plikus@uci.edu
Phone 949-824-1260
Organization name University of California, Irvine
Department Developmental and Cell Biology
Street address 845 Health Sciences Road
City Irvine
State/province California
ZIP/Postal code 92697
Country USA
 
Platform ID GPL13112
Series (1)
GSE140956 The Msi1-mTOR pathway drives the pathogenesis of Paget's disease
Relations
BioSample SAMN13383583
SRA SRX7213612

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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