|
| Status |
Public on Dec 04, 2017 |
| Title |
B16F10 shLSD1 |
| Sample type |
SRA |
| |
|
| Source name |
B16F10 melanoma cell line
|
| Organism |
Mus musculus |
| Characteristics |
treatment: shLSD1
cell line: B16F10
cell type: melanoma
|
| Treatment protocol |
Cells were transduced with shLSD1, shJMJD2C or scrambled shRNA construct as control.
|
| Growth protocol |
Cells were cultured in DMEM medium with 10% FBS and penicillin/streptomycin in 37°C incubator.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Qiagen RNeasy Plus Mini Kit.
Libraries were prepared by BGI (Hongkong).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
Computational rRNA depletion using SortMeRNA version 2.1
RNA-seq reads were aligned to the GRCm38 Ensembl release 88 reference genome using STAR RNA-seq aligner 2.5.2b with --twopassMode Basic
sam files were converted to BAM format using Samtools version 0.18
Transcript abundance was quantified using the summarizeOverlaps function in the R/Bioconductor package GenomicAlignments. Counting mode was set to "Union"
Raw transcript counts were transformed to log2-scale using the rlog function from the R/Bioconductor package DESeq2
Genome_build: GRCm38 Ensembl release 88
Supplementary_files_format_and_content: F17FTSEUHT0688_mouse_Counts.txt.gz contains a data matrix of raw transcript counts; F17FTSEUHT0688_mouse_RLOG.txt.gz contains log2 expression values generated by rlog from the DESeq2 package in R/Bioconductor. Both files are tab-delimited with samples in columns and features in rows.
|
| |
|
| Submission date |
Oct 18, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Maja Milanovic |
| E-mail(s) |
[email protected]
|
| Organization name |
Charite University Medicine, Berlin
|
| Department |
Hematology and Oncology
|
| Lab |
Clemens Schmitt
|
| Street address |
Augustenburgerplatz 1
|
| City |
Berlin |
| ZIP/Postal code |
13353 |
| Country |
Germany |
| |
|
| Platform ID |
GPL23479 |
| Series (2) |
| GSE105138 |
Gene Expression Profiling of one melanoma cell line after shRNA-mediated knockdown of JMJD2C or LSD1 |
| GSE105166 |
Gene Expression Profiling of human and mouse melanoma cell lines after shRNA-mediated knockdown of JMJD2C or LSD1 |
|
| Relations |
| BioSample |
SAMN07810194 |
| SRA |
SRX3298767 |
