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Status |
Public on Feb 02, 2023 |
Title |
C129_B3_L1_38wUW_RepN |
Sample type |
SRA |
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|
Source name |
Murine Epidermal cells
|
Organism |
Mus musculus |
Characteristics |
strain: CBA C57BL/6 mixed cell type: Keratinocytes plate: C129 population: L1 time: 38wUW replicate: RepN batch: Replicate1 batch_alt: Replicate2
|
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).
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|
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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.
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|
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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 |
SAMN26311256 |
SRA |
SRX14313478 |