GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM4378540 Query DataSets for GSM4378540
Status Public on Apr 11, 2020
Title scRNA-seq_P7
Sample type SRA
Source name tail interfollicular epidermal basal cells at postnatal day 7
Organism Mus musculus
Characteristics strain: Lgr5DTR-EGFP mice (Tian et al., Nature, 2011)
age: postnatal day 7
tissue: tail epidermis
cell type: FACS sorted basal cells
Treatment protocol no treatment
Extracted molecule total RNA
Extraction protocol After incubation in HBSS (Gibco) 0,25% trypsin (Gibco) at 4°C overnight, tail epidermis was separtaed from the dermis and cells were mechanically dissociated, stained with PE-conjugated anti-a6-integrin (clone GoH3; 1:200, ebioscience) and bulge cells were stained with biotinylated CD34 (clone RAM34; 1:50, BD Biosciences) and APC-conjugated streptavidin (BD Biosciences). Basal cells were enriched using EGFP negative, CD34 negative and integrin a6 positive gating and FACS sorted. After sorting, 6000 cells were loaded onto each channel of the Chromium Single Cell 3’ microfluidic chips (V2-chemistry, PN-120232, 10X Genomics) and individually barcoded with a 10X Chromium controller according to the manufacturer’s recommendations (10X Genomics). RNA from the barcoded cells was reverse transcribed, followed by amplification, shearing 5′ adaptor and sample index attachment.
The libraries were prepared using the Chromium Single Cell 3’ Library Kit (V2-chemistry, PN-120233, 10X Genomics), quantified using a low coverage Illumina NextSeq 550 run and sequenced on an Illumina NovaSeq
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Data processing Read Alignment - CellRanger (version 3.0.2)
Cell-cycle assignment - Scran (1.10.1)
UMAP dimensionality reduction - Seurat (3.0.1)
Normalization - Seurat (3.0.1)
Gene regulatory network analysis - SCENIC (0.9.9+2.gcaded79)
Genome_build: mm10-1.2.0
Supplementary_files_format_and_content: R Rds objects; scRNAseq CellRanger output; SCENIC AUC Matrix; SCENIC regulon definitions
Submission date Mar 04, 2020
Last update date Apr 11, 2020
Contact name Cédric Blanpain
Phone +32 2 555 3015
Organization name Université Libre de Bruxelles
Lab Laboratory of Stem Cells and Cancer
Street address 808 route de Lennik
City Brussel
ZIP/Postal code 1070
Country Belgium
Platform ID GPL24247
Series (1)
GSE146122 Single Cell RNA-sequencing of murine tail interfollicular epidermis basal cells at postnatal days 7, 30 and in adult
BioSample SAMN14280836
SRA SRX7847261

Supplementary file Size Download File type/resource
GSM4378540_P7_SEURAT_FILTERED_ANNOTATED.Rds.gz 784.1 Mb (ftp)(http) RDS
GSM4378540_p7.auc_mtx.csv.gz 19.3 Mb (ftp)(http) CSV
GSM4378540_p7.barcodes.tsv.gz 49.1 Kb (ftp)(http) TSV
GSM4378540_p7.features.tsv.gz 272.8 Kb (ftp)(http) TSV
GSM4378540_p7.matrix.mtx.gz 85.4 Mb (ftp)(http) MTX
GSM4378540_p7.regulons.csv.gz 5.4 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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