|
| Status |
Public on Feb 22, 2022 |
| Title |
sgPHF8-3-B |
| Sample type |
SRA |
| |
|
| Source name |
Melanoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: SKMEL-147 melanoma cell line
guide: sgPHF8 3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAeasy Mini Kit (Qiagen), according to the manufacturer's instructions.
RNA quality was defined on an Agilent 2100 Bioanalyzer, then processed with Ribo-Zero rRNA Removal Kit (Illumina) to remove rRNA, and further processed into sequencing libraries using the Illumina ScriptSeq Complete Gold kit following manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The sequencing reads were aligned to the human genome using the splice-aware STAR aligner.
Likely PCR duplicates were removed with Picard MarkDuplicates tool.
Htseq package was utilized to generate counts for each gene.
The raw counts were normalized using the DESeq2 R package.
Genome_build: hg19
Supplementary_files_format_and_content: CSV files contain raw and normalized counts for all genes and samples.
|
| |
|
| Submission date |
Feb 16, 2022 |
| Last update date |
Feb 22, 2022 |
| Contact name |
Igor Dolgalev |
| Organization name |
NYU Grossman School of Medicine
|
| Street address |
550 1st Ave
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE196905 |
The histone demethylase PHF8 regulates TGFβ signaling and promotes melanoma metastasis [RNA-seq] |
| GSE196906 |
The histone demethylase PHF8 regulates TGFβ signaling and promotes melanoma metastasis |
|
| Relations |
| BioSample |
SAMN25999283 |
| SRA |
SRX14205820 |
