|
| Status |
Public on Jan 04, 2021 |
| Title |
Growing_RNA-seq [SLX-12349.D706_D501] |
| Sample type |
SRA |
| |
|
| Source name |
Keratinocyte_K23
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Skin-derived primary keratinocyte
passage: 5
condition: Growing
|
| Treatment protocol |
To induce differentiation in culture, keratinocytes were treated with 500 nM of phorbol 12-myristate 13-acetate (PMA, Sigma, P8139) for 48 h after become confluent.
|
| Growth protocol |
Keratinocytes were cultured in Epilife (Gibco) suppremented with human keratinocyte growth supprement (HKGS, Gibco).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For ChIP-seq, lysates were cralified from sonicated nuclei and histone-DNA complexes were isolated with antibody. For RNA-seq, RNA was purified from using the Qiagen RNeasy plus kit according to the manufacturer's instructions.
For ChIP-seq, libraries were prepared using the NEB-Next Ultra II DNA Library Prep Kit (E7645, New England Biolabs) according to the manufacturer's instructions. For RNA-seq, libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Reads were mapped to the human reference (hg19). ChIP-seq and ATAC-seq samples were mapped using BWA (version 0.7.12) and RNA-seq samples using STAR aligner (version 2.6.0c).
Low quality reads (mapping quality less than 20) as well as known adapter contamination were filtered out using Cutadapt (version 1.10.0).
H3K27AC, H3K27me3 and ATAC-seq samples: Average fragment size was determined using the ChIPQC Bioconductor package, and peak calling was performed with MACS2 (version 2.1.0), using fragment size as an extension size (--extsize parameter).
H3K9me3 samples: Enriched domains were called with EDD
ChIP-seq and ATAC-seq normalised coverage files (.bw) were generated using THOR.
RNA-seq counts were calculated using Rsubread.
Genome_build: hg19
Supplementary_files_format_and_content: .bw = coverage files
Supplementary_files_format_and_content: .narrowPeak/.bed = peak files
Supplementary_files_format_and_content: .txt = counts
|
| |
|
| Submission date |
Apr 29, 2019 |
| Last update date |
Jan 04, 2021 |
| Contact name |
Shamith Samarajiwa |
| Organization name |
Imperial College London
|
| Department |
Genetics and Genomics Section Department of Metabolism, Digestion and Reproduction
|
| Lab |
Computational Biology & Data Science
|
| Street address |
ICTEM Building, Hammersmith Campus, Du Cane Road,
|
| City |
London |
| ZIP/Postal code |
W12 0NN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE130457 |
Aberrant gene expression leakage from linage-specific heterochromatic loci during senescence |
|
| Relations |
| BioSample |
SAMN11528444 |
| SRA |
SRX5766170 |
