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Sample GSM5922254 Query DataSets for GSM5922254
Status Public on Feb 02, 2023
Title C128_H9_L1_38wUW_RepM
Sample type SRA
 
Source name Murine Epidermal cells
Organism Mus musculus
Characteristics strain: CBA C57BL/6 mixed
cell type: Keratinocytes
plate: C128
population: L1
time: 38wUW
replicate: RepM
batch: Replicate2
batch_alt: Replicate1
Treatment protocol Lrig1-EGFP-ires-CreERT2 Rosa26-fl/STOP/fl-tdTomato mice received a single topical application of hydroxytamoxifen on tail skin prior to wounding.
Extracted molecule total RNA
Extraction protocol Flow citometry was used to sort tomato positive epidermal cells
Full length single cell RNA-seq was performed using a modified version of the Smart-seq2 protocol. Briefly, individual cells are sorted into 96 well plates containing lysis buffer in presence of RNase inhibitor, dNTPs and OligodT. Reverse transcription of the polyadenylated RNA will be performed with SuperScriptII and Template Switching Oligos. The resulting cDNA will be amplified with 25 cycles of PCR and libraries will be prepared for sequencing with standard NexteraXT Illumina protocol. Libraries were sequenced on Illumina NextSeq 500 System (single-end 75bp reads).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Following quality controls , reads were mapped to the Mus musculus transcriptome (ENSEMBL version 101) using Salmon v 0.13.1 and RNA-seq data were analysed using Seurat packages (v 4.0.1) on R (v 4.0.3).
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: Tab-delimited text file of gene expression read counts matrix per gene/cell.
 
Submission date Feb 28, 2022
Last update date Feb 02, 2023
Contact name Andrea Lauria
E-mail(s) andrea.lauria@unito.it
Organization name University of Turin
Department Life Sciences and Systems Biology
Lab Functional Genomics, Epigenomics - S. Oliviero
Street address Via Accademia Albertina, 13
City Turin
ZIP/Postal code 10123
Country Italy
 
Platform ID GPL19057
Series (2)
GSE197588 Wound memory of epidermal stem cells [scRNAseq L1-aged]
GSE197590 Wound memory of epidermal stem cells
Relations
BioSample SAMN26311271
SRA SRX14313399

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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