|
| 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 |
