|
| Status |
Public on Dec 18, 2023 |
| Title |
Human primary keratinocytes, not treated, 24 h, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
epidermis
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: epidermis
cell line: cultured primary cells
cell type: keratinocyte
treatment: not treated
|
| Treatment protocol |
HPK were treated, or not, with S1P (1 μM) for 24 h
|
| Growth protocol |
HPK were grown in Dermalife K medium (Cellsystems) supplemented with 100 UI/ml penicillin and 100 µg/ml streptomycin, with medium changes thrice a week. Experiments were performed on low passage (≤ 3) keratinocytes.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the Truseq Stranded mRNA Kit and IDT for Illumina Truseq RNA UD Indexes from Illumina, following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Illumina Truseq adapter, polyA and polyT sequences were trimmed with cutadapt v2.3
Trimmed sequences were aligned to human genome version 38 (hg38) using bowtie2 aligner with parameters according to ENCODE long RNA-seq pipeline (https://github.com/ENCODE-DCC/long-rna-seq-pipeline)
Gene expression levels were quantified using RSEM v1.3.1
Ensembl gene annotation version 93 was used in the alignment and quantification steps
RNA-seq sequence, alignment and quantification quality was assessed using FastQC v0.11.7 (https://www. bioinformatics.babraham.ac.uk/projects/fastqc/).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include Expected counts values for each Sample
|
| |
|
| Submission date |
Apr 19, 2023 |
| Last update date |
Dec 18, 2023 |
| Contact name |
Nathalie ANDRIEU-ABADIE |
| E-mail(s) |
nathalie.andrieu@inserm.fr
|
| Organization name |
INSERM
|
| Department |
UMR1037
|
| Lab |
The Cancer Research Center of Toulouse
|
| Street address |
2 Avenue Hubert Curien
|
| City |
Toulouse |
| ZIP/Postal code |
31037 |
| Country |
France |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE230050 |
Effect of S1P on gene expression in human primary keratinocytes |
|
| Relations |
| BioSample |
SAMN34249634 |
| SRA |
SRX20009302 |
