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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 11, 2020 |
| Title |
scRNA-seq_P7 |
| Sample type |
SRA |
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| Source name |
tail interfollicular epidermal basal cells at postnatal day 7
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| 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
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| Treatment protocol |
no treatment
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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
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| Submission date |
Mar 04, 2020 |
| Last update date |
Apr 11, 2020 |
| Contact name |
Cédric Blanpain |
| E-mail(s) |
cedric.blanpain@ulb.ac.be
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| Phone |
+32 2 555 3015
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| Organization name |
Université Libre de Bruxelles
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| Lab |
Laboratory of Stem Cells and Cancer
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| Street address |
808 route de Lennik
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| City |
Brussel |
| ZIP/Postal code |
1070 |
| Country |
Belgium |
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| 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 |
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| Relations |
| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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