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Sample GSM2061144 Query DataSets for GSM2061144
Status Public on May 20, 2016
Title SLNCR1 cons rep1
Sample type SRA
 
Source name A375_SLNCR1_conserved
Organism Homo sapiens
Characteristics cell line: A375
tissue: skin
disease: malignant melanoma
Treatment protocol 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).
Growth protocol A375 cells were maintained in DMEM plus 10% FBS.
Extracted molecule total RNA
Extraction protocol 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®.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description processed data file: SLNCR1cons_vs_vector.deseq.txt
Data processing 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/).
Genome_build: hg19
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).
 
Submission date Feb 13, 2016
Last update date May 15, 2019
Contact name Carl Novina
E-mail(s) carl_novina@dfci.harvard.edu
Organization name Dana-Farber Cancer Institute
Department Cancer Immunology
Lab Carl Novina
Street address 450 Brookline Ave
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL18573
Series (2)
GSE77901 RNA-Seq of SLNCR1 over-expression in the melanoma cell line A375
GSE77903 RNA-Seq of over-expression and knockdown of the lncRNA SLNCR1 in melanoma cells
Relations
SRA SRX1584396
BioSample SAMN04504683

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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