|
| 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) |
[email protected]
|
| 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 |
