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Status |
Public on Nov 06, 2020 |
Title |
Mouse 1 Abdomen Control [M1AC] |
Sample type |
SRA |
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Source name |
Abdomen Skin Control
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Organism |
Mus musculus |
Characteristics |
strain: CD1 tissue: Skin anatomical site: Abdomen treatment: Control
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Treatment protocol |
For wound experiments, age-matched mice (7 weeks, coordinated in telogen) were anaesthetised and provided analgesic, and then shaved and subjected to one (cheek) or two (abdomen/back) 2mm (diameter)-thickness excisional wounds at a single site. After 3 days, mice were sacrificed and wound (or adjacent healthy control) tissue was collected using a 2mm punch biopsy.
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Growth protocol |
All experiments were conducted according to UK Home Office regulations. CD1 mice from an in-house colony were maintained with free access to food and water and a 12h light-dark cycle.
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Extracted molecule |
total RNA |
Extraction protocol |
Whole tissue (flash frozen in liquid nitrogen upon harvest) was first homogenised in lysis buffer with the help of a QIAshredder. Total RNA was then extracted from whole tissue using a Qiagen RNeasy Total RNA kit. RNA libraries were prepared for sequencing using standard Illumina protocols (performed by BGI)
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
BGISEQ-500 |
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Description |
M1AC
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Data processing |
Sequencing Reads Filtering: Removed low quality reads (more than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) to get the clean reads. Used BGI internal software SOAPnuke versions v1.5.2, parameters: -l 15 -q 0.4 -n 0.01 -A 0.25, website: https://github.com/BGI-flexlab/SOAPnuke Mapping: HISAT2 (version v2.0.4) was used to map clean reads onto reference genome mm10 (parameters: --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000 Gene Expression Analysis: Clean reads were mapped to reference using Bowtie2 (v2.2.5), and then calculate gene expression level with RSEM (v1.2.12). Differentially expressed genes (DEGs): DEGs were identified with DEseq2.DEseq2 is based on the negative binomial distribution, performed as described at Love, M. I., Huber, W. & Anders, S. Genome Biol. 15, 550 (2014). Genome_build: mm10 Supplementary_files_format_and_content: Format: tab-delimited text; Content: Rows=genes, Columns=GeneID, TranscriptID, Symbol, Description, and all 24 Samples Supplementary_files_format_and_content: Format: tab-delimited text; Content: Rows=genes, Columns=9 pair-wise comparisons [log2 fold change (left column) and adjusted pvalue (right column)]
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Submission date |
Jun 04, 2020 |
Last update date |
Nov 06, 2020 |
Contact name |
Tanya J Shaw |
E-mail(s) |
tanya.shaw@kcl.ac.uk
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Organization name |
King's College London
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Department |
Centre for Inflammation Biology & Cancer Immunology
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Street address |
Guy's Campus, New Hunt's House, Great Maze Pond
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City |
London |
ZIP/Postal code |
SE1 1UL |
Country |
United Kingdom |
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Platform ID |
GPL23479 |
Series (1) |
GSE151850 |
Anatomical diversity of dermis in homeostasis and wound repair |
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Relations |
BioSample |
SAMN15105177 |
SRA |
SRX8474531 |
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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