|
| Status |
Public on Mar 25, 2024 |
| Title |
3_TNF-TGF_D14 |
| Sample type |
SRA |
| |
|
| Source name |
GLO
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: GLO
vector: NA
treatment: 7% FBS + TNF-alpha and TGF-beta (14 days)
cell type: Melanoma short-term cultures
|
| Treatment protocol |
Cells were treated with TNF-α (100 ng/mL) or TNF-α (100 ng/mL) + TGF-β (10 ng/mL) for 7 and 14 days, the treatment was replaced every 3 days.
|
| Growth protocol |
Cells were seeded in 6 well plates and cultivated in media containing TNF-α (100 ng/mL) or TNF-α (100 ng/mL) + TGF-β (10 ng/mL).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the RNeasy Kit (QIAGEN) following to manufacturer's recommendations. RNA was quantified and integrity was measured by optic density using a 2100 BioAnalyzer.
Libraries were prepared with the TruSeq poly-A+ kit from Illumina.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
GLO_J14_3
mRNA
|
| Data processing |
Raw sequencing reads were aligned on the human genome (GRCh38) with STAR (v2.7.8a), with the annotation of known genes from gencode v37.
Gene expression was quantified using Salmon (1.4.0) and the annotation of protein coding genes from gencode v37.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file with normalized expression (log2 TPM) from salmon for each sample.
|
| |
|
| Submission date |
Oct 30, 2023 |
| Last update date |
Mar 25, 2024 |
| Contact name |
Julie CARAMEL |
| E-mail(s) |
[email protected]
|
| Phone |
+33426556705
|
| Organization name |
Cancer Research Center of Lyon
|
| Street address |
28 Rue Laennec
|
| City |
LYON |
| ZIP/Postal code |
69008 |
| Country |
France |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE246603 |
ZEB1 controls a lineage-specific transcriptional program essential for melanoma cell state transitions [RNA-seq] |
| GSE246673 |
ZEB1 controls a lineage-specific transcriptional program essential for melanoma cell state transitions |
|
| Relations |
| BioSample |
SAMN38052234 |
| SRA |
SRX22323691 |
