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Sample GSM3110286 Query DataSets for GSM3110286
Status Public on Jun 29, 2018
Title K5-1st_S021
Sample type SRA
 
Source name Skin
Organism Homo sapiens
Characteristics tissue: Skin
diagnosis: keloid
age: 24
Sex: male
time point: day 0
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using RNeasy Plus Universal kit (Qiagen, Valencia, USA) and miRNAs retained according to the manufacturer’s protocol
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description K5-1st_S021_R1_.fastq.gz
K5-1st_S021_R2_.fastq.gz
Data processing Whole transcriptome RNA-Seq libraries were prepared on the Agilent Bravo liquid handling system using a modification of the Agilent Sureselect stranded RNA kit (Catalog 9691B). Sequencing was conducted on HiSeq2500 and HiSeq3000 (Illumina, San Diego)
Sequencing reads were aligned against the human genome sequence (hg38) using hisat2. Reads with a MAPQ (mapping quality) below 10 [-10 X log10 Pr(mapping position is wrong=0.100] and PCR duplicate reads were removed with Samtools package. The UCSC hg38 genome annotation was used to generate gene count tables for each sample using the GenomicAlignments library in R. Gene counts for the technical replicates were added together and data were normalized for library size correction using DESeq2
Principal Component Analysis (PCA) on the normalized gene counts was performed to ensure the homogeneity of the data and to exclude any potential batch effects among sequencing runs. RNA differential expression (DE) analysis was performed with the glmmADMB package in R using a mixed effect generalized linear model with a random intercept for each patient from the negative binomial family.
Genome_build: hg38
Supplementary_files_format_and_content: csv file with raw or normalized counts
 
Submission date Apr 24, 2018
Last update date Jul 24, 2018
Contact name John Alexander McGrath
E-mail(s) john.mcgrath@kcl.ac.uk
Organization name King's College London
Department St John's Institute of Dermatology
Lab St John's Institute of Dermatology
Street address Great Maze Pond
City London
ZIP/Postal code SE1 9RT
Country United Kingdom
 
Platform ID GPL21290
Series (2)
GSE113619 Time series integrative analysis of RNA-Seq and miRNA expression data reveals key biologic pathways during keloid formation [RNA-seq]
GSE113621 Time series integrative analysis of RNA-Seq and miRNA expression data reveals key biologic pathways during keloid formation
Relations
BioSample SAMN08863003
SRA SRX3882458

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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