|Public on May 20, 2016
|SLNCR1 cons rep1
|cell line: A375
disease: malignant melanoma
|Cells were transfected with pcDNA3.1(-) empty vector control, or vector expressing SLNCR1, SLNCR1 delta conserved, or SLNCR1 conserved 24 hours post-seeding using Lipofectamine 2000 (Invitrogen).
|A375 cells were maintained in DMEM plus 10% FBS.
|Cells were harvested 48 hours post-transfection RNA was isolated using Trizol® (Life Technologies) and Qiagen RNeasy Mini Kit and treated with DNase.
RNA was selected using NEBNext® PolyA mRNA Magnetic Isolation Module and libraries were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®.
|Illumina NextSeq 500
|processed data file: SLNCR1cons_vs_vector.deseq.txt
|Read alignment to the hg19 reference genome/transcriptome was performed with STAR (http://bioinformatics.oxfordjournals.org/content/29/1/15).
Raw sequence files converted to base-calls by the sequencer software
Sequencing reads aligning to unique exons are summed within each gene locus. Counting is performed by featureCounts software (http://bioinformatics.oxfordjournals.org/content/30/7/923.full.pdf). Reads located in regions where genomic features overlap are ignored since they cannot be definitively assigned to a single transcript.
Read-count normalization is performed by DESeq software (http://genomebiology.com/2010/11/10/R106/).
Supplementary_files_format_and_content: tab delimited text files including GeneID, BaseMean(Average), BaseMean Replicate1, BaseMean Relicate2, fold change, Log2 fold change, p-value and adjusted p-value. For these DESEq output files, Basemean A refers to vector only while Basemean B refers to expression of either SLNCR1, SLNCR1 delta cons or SLNCR1 cons (as denoted in the file title).
|Feb 13, 2016
|Last update date
|May 15, 2019
|Dana-Farber Cancer Institute
|450 Brookline Ave
|RNA-Seq of SLNCR1 over-expression in the melanoma cell line A375
|RNA-Seq of over-expression and knockdown of the lncRNA SLNCR1 in melanoma cells