|
| Status |
Public on Sep 15, 2021 |
| Title |
PRO 3D 2 |
| Sample type |
SRA |
| |
|
| Source name |
Melanoma
|
| Organism |
Danio rerio |
| Characteristics |
cell line: ZMEL1-PRO
cell type: Melanoma
culture method: 3D
|
| Growth protocol |
ZMEL1 was grown in Corning Ultra-Low Attachment 6-well plates (#3471) at 28ºC in a humidified incubator in DMEM (Gibco #11965) supplemented with 10% FBS (Seradigm), 1X penicillin/streptomycin/glutamine (Gibco #10378016), and 1X GlutaMAX (Gibco #35050061)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted with the RNeasy Plus Mini kit with QiaShredder (Qiagen)
Purified RNA was delivered to GENEWIZ (South Plainfield, NJ) for mRNA preparation with the TruSeq RNA V2 kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
quality control with FASTQC (Babraham Bioinformatics)
trimming with TRIMMOMATIC
reads were aligned to GRCz10 (Ensembl version 81) using STAR with --quantMode GeneCounts
quality control via SeQC
Differential expression was calculated with DESeq2
Genome_build: GRCz10, Ensembl version 81
Supplementary_files_format_and_content: CSV file with raw counts from STAR
|
| |
|
| Submission date |
Jun 02, 2020 |
| Last update date |
Sep 15, 2021 |
| Contact name |
Nathaniel R Campbell |
| Organization name |
Memorial Sloan Kettering Cancer Center
|
| Street address |
417 E 68th St, Z-1325
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL18413 |
| Series (2) |
| GSE151678 |
Cell state diversity promotes metastasis through heterotypic cluster formation in melanoma [3D culture] |
| GSE151679 |
Cell state diversity promotes metastasis through heterotypic cluster formation in melanoma |
|
| Relations |
| BioSample |
SAMN15086630 |
| SRA |
SRX8456050 |
