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Sample GSM4592313

Query DataSets for GSM4592313

Status

Public on Nov 06, 2020

Title

Mouse 3 Back Control [M3BC]

Sample type

SRA

Source name

Back Skin Control

Organism

Mus musculus

Characteristics

strain: CD1
tissue: Skin
anatomical site: Back
treatment: Control

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.

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.

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)

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

BGISEQ-500

Description

M3BC

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)]

Submission date

Jun 04, 2020

Last update date

Nov 06, 2020

Contact name

Tanya J Shaw

E-mail(s)

tanya.shaw@kcl.ac.uk

Organization name

King's College London

Department

Centre for Inflammation Biology & Cancer Immunology