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| Status |
Public on Dec 07, 2016 |
| Title |
PWD15 Rep1 |
| Sample type |
SRA |
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| Source name |
Cutaneous wound myofibroblast
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| Organism |
Mus musculus |
| Characteristics |
background strain: Mixed background
cell type: Cutaneous wound myofibroblast
post-wounding day: 15
genotype: Sm22-Cre;tdTomato
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cutaneous wound tissues were harvested and dissegragated into single cell suspensions with collagenase. Cells were FACS sorted as viable tdTomatoHi directly into lysis buffer. Total RNA was isolated using RNEasy Micro Kit as per manufacturer's protocols. RNAs with optimal quality (RIN>8.8) were considered for library construction.
RNA libraries were prepared for sequencing using standard SMART-seq2 protocols. 1. S. Picelli et al., Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nature methods 10, 1096-1098 (2013). 2. S. Picelli et al., Full-length RNA-seq from single cells using Smart-seq2. Nature protocols 9, 171-181 (2014).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
protocol: SMART-seq2
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| Data processing |
RSEM was used for alignment, mapping and quantification
Reads were not trimmed for adaptor sequence. Sequenced reads were aligned, mapped and quantified to the mouse genome (mm10/vM4) using RSEM v1.12.2 with standard parameters. (B. Li, C. N. Dewey, RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC bioinformatics 12, 323 (2011).).
Genome_build: mm10
Supplementary_files_format_and_content: Excel file Supplement_Table_S6.xlsx includes FPKM values for each sample with a pseudocount of 1. Supplement_Table_S5.xlsx includes data clustering with fold-changes and gene ontology.
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| Submission date |
Jul 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Maksim V Plikus |
| E-mail(s) |
plikus@uci.edu
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| Phone |
949-824-1260
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| Organization name |
University of California, Irvine
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| Department |
Developmental and Cell Biology
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| Street address |
845 Health Sciences Road
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| City |
Irvine |
| State/province |
California |
| ZIP/Postal code |
92697 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE84256 |
Fat cells regenerate from myofibroblasts during wound healing |
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| Relations |
| BioSample |
SAMN05372093 |
| SRA |
SRX1925602 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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