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| Status |
Public on Dec 21, 2022 |
| Title |
TGF.SM31.rep1 |
| Sample type |
SRA |
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| Source name |
Spontaneously immortalized human keratinocyte cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HaCaT cells
treatment: TGF-β1 (10ng/ml) + SM (31.25 µg/ml)
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated from HaCaT cells using mirVanaTM miRNA isolation kit (Ambion, Life Technologies, Cat #AM1560)
Libraries were constructed using the Illumina mRNA Stranded Kit, according to the manufacturer recommandations
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Image analysis, base calling and demultiplexing were performed using RTA 2.4.6 and bcl2fastq 2.18.12
Adapter sequences were trimmed with Cutadapt-1.15, only reads longer than 10 bp were kept for analysis
Sequences were aligned to the Human genome with TopHat2 2.1.1 using default parameters
Uniquely mapped reads were assigned to genes with FeatureCounts- subread v.1.5.2
Differential expression analysis was performed with DESeq2,
Genome_build: Hg 19 gencode v.17
Supplementary_files_format_and_content: Matrix table with normalized abundance measurements for every gene and every sample (output from DESeq2)
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| Submission date |
Nov 30, 2020 |
| Last update date |
Dec 21, 2022 |
| Contact name |
Patrick Baril |
| E-mail(s) |
patrick.baril@cnrs.fr
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| Organization name |
Centre de Biophysique Moléculaire, CNRS-UPR4301
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| Street address |
Rue Charles Sadron
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| City |
Orléans |
| ZIP/Postal code |
45071 |
| Country |
France |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE162336 |
Global transcriptome analysis of long RNA molecules expressed in human keratinocyte cell line HaCaT pre-treated with TGF-β1 in response to silymarin, a natural plant extract involved in skin tissue regeneration |
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| Relations |
| BioSample |
SAMN16956030 |
| SRA |
SRX9605517 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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