|
| Status |
Public on May 08, 2024 |
| Title |
YUCHIME_siITGA3_1_S4 |
| Sample type |
SRA |
| |
|
| Source name |
metatastic melanoma cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: metatastic melanoma cells
gender: M
cohort: Wistar
genotype/variation: siRNA ITGA3
|
| Growth protocol |
Primary melanocytes were grown in melanocyte growth media. WM35, 983, 902, and 1552 cell lines were grown in 2% tumor media. YUPEET and YUCHIME cell lines were grown in basic FGF media.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were pelleted and RNA was harvested using the Qiagen Rneasy kit. Illumina TruSeq Stranded Total RNA Sample Prep Kit with Ribo-Zero (for removal of rRNA) (Cat#20020598) was used with 1.5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
We first assessed the quality of paired-end reads with FASTQC (v0.11.8).
we filtered reads with BBDUK from BBTOOLS (v37.53) to remove adapters, known artefacts, and quality trimmed (PHRED quality score <10).
Reads that became too short after trimming (N<60 bp) were discarded. Singleton reads (i.e., reads whose mate has been discarded) were not retained.
We estimated the transcript-level quantification of cleaned RNA-seq data using SALMON (v1.0.0) by a quasi-mapping on Homo sapien sapien hg38.
Assembly: Human hg38
Supplementary files format and content: SALMON - format - .sf - TMM and read counts
|
| |
|
| Submission date |
Mar 11, 2022 |
| Last update date |
May 08, 2024 |
| Contact name |
Tiphaine Christiane Martin |
| E-mail(s) |
[email protected]
|
| Phone |
2128248403
|
| Organization name |
Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute
|
| Department |
Oncological Sciences
|
| Lab |
Parsons
|
| Street address |
1470 Madison Ave
|
| City |
New York |
| State/province |
75459 |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE198427 |
An epigenetic gene signature underlies phenotype switching in early stage melanomas [YUCHIME] |
| GSE198432 |
An epigenetic gene signature underlies phenotype switching in early stage melanomas. |
|
| Relations |
| BioSample |
SAMN26581368 |
| SRA |
SRX14438530 |
