|
| Status |
Public on Oct 30, 2023 |
| Title |
839T_siControl_3 |
| Sample type |
SRA |
| |
|
| Source name |
Skin
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Skin
treatment: siRNA Control
|
| Treatment protocol |
Cells were transfected with ON-TARGETplus Non-targeting Control Pool or ON-TARGETplus B7H3 siRNA (Dharmacon) for 72 hours.
|
| Growth protocol |
Human melanoma cell lines were cultured using standard methods.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from samples using the RNeasy Protect Mini Kit (Qiagen). The RNA Integrity Number of each sample was determined using the 2100 Bioanalyzer instrument (Agilent Technologies). Samples were selected with stringent criteria based on RNA Integrity Number of 7.0 or greater, and a minimum of 500 ng of total RNA. Total RNA was subjected to ribosomal RNA depletion and further used as input for library construction by the Illumina TruSeq Standard Total RNA library Pre Gold kit (Illumina).
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 |
| |
|
| Description |
siRNA Control treatment to human melanoma cell line 839T, Replicate 3
|
| Data processing |
Reads were mapped to the human genome using STAR vSTAR_2.5.2a
Counts of reads mapping to each gene were quantified using featureCounts utility from the Subread package v1.4.6-p5
Expression as log(counts per million) was computed using edgeR v.3.30 package for R v.4.0.2
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include raw counts and expression for each sample
|
| |
|
| Submission date |
Jul 29, 2020 |
| Last update date |
Oct 30, 2023 |
| Contact name |
Tiphaine Christiane Martin |
| E-mail(s) |
tiphaine.martin@mssm.edu
|
| 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) |
| GSE155394 |
Combined blockade of B7-H3 and CD47 immune checkpoints is a new therapeutic strategy for β-catenin driven melanomas [transfection] |
| GSE161180 |
Combined blockade of B7-H3 and CD47 immune checkpoints is a new therapeutic strategy for β-catenin driven melanomas |
|
| Relations |
| BioSample |
SAMN15670608 |
| SRA |
SRX8845866 |
