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Sample GSM5606755 Query DataSets for GSM5606755
Status Public on Jun 07, 2023
Title control skin cells
Sample type SRA
 
Source name P53 skin cells
Organism Mus musculus
Characteristics cells: epithelial and dermal cells
strain: C57BL/6
treatment: untreated
Treatment protocol miR-205 inducible mouse was feed Doxcyclin chow for 4 days from P49-P53.
Extracted molecule total RNA
Extraction protocol Gender matched mice (Ctrl and miR-205Ind) harboring a K14-H2BGFPallele were fed doxycycline for 4 days and euthanized to collect back skin samples. Hair coats were shaved and removed. Subcutaneous fat was removed, and back skin samples were minced into small pieces and incubated with 0.25% collagenase (Worthington, LS004188) in 10 mL 1x HBSS buffer at 37°C for 2 hours with rotation. After collagenase treatment, 10 mL cold PBS was added, and sample suspension was centrifugated at 400 g for 10 minutes at 4°C to get the pellet. The pellet was resuspended with 5 ml pre-warmed 0.25% trypsin/EDTA (Gibco) for 7 minutes at 37°C and the digestion was blocked by adding 10 mL cold 1x PBS with 3% chelated FBS. The suspension was extensively triturated with a 25 ml pipette and filtered through a 40 m cell strainer, followed by centrifugation at 400 g for 5 minutes at 4°C. The pelleted cells were resuspended in cold 1x PBS with 3% chelated FBS. Suspended cells were incubated with appropriated antibodies for 1 hour on ice. After washing away unbounded antibodies, DAPI was used to exclude dead cells. Cells from both control and miR-205 inducible animals were collected from FACS sorting machine with cell surface proteins and H2BGFP signals such that the epidermal cells, hair follicle cells and dermal cells are 3: 5: 2 ratio.
Single-cell RNA-seq was performed according to manufacturer’s instruction (10X Genomics). Each sample was targeted to obtain ∼5,000 cells.
single cell RNA-seq
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing The Cell Ranger Single-Cell Software Suite was used to perform barcode processing and single-cell 3’ gene counting (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome).
Genome_build: mm10
Supplementary_files_format_and_content: tsv and matrix file
 
Submission date Sep 30, 2021
Last update date Jun 07, 2023
Contact name Rui Yi
E-mail(s) yir@northwestern.edu
Organization name Northwestern University
Department Pathology, Feinberg School of Medicine
Lab Yi Lab
Street address 765 N FAIRBANKS CT
City Chicago
State/province Illinois
ZIP/Postal code 60611
Country USA
 
Platform ID GPL21103
Series (2)
GSE185115 Single cell RNA-seq analysis of mouse miR-205 inducible adult back skin
GSE185117 RNA-seq for miR-205 inducible hair follicle stem cells and ScRNAseq for miR-205 inducible back skin samples
Relations
BioSample SAMN21924094
SRA SRX12418551

Supplementary file Size Download File type/resource
GSM5606755_Ctrl_barcodes.tsv.gz 23.8 Kb (ftp)(http) TSV
GSM5606755_Ctrl_features.tsv.gz 272.8 Kb (ftp)(http) TSV
GSM5606755_Ctrl_matrix.mtx.gz 43.6 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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