|
| Status |
Public on Nov 25, 2020 |
| Title |
RNAseq_MM3 |
| Sample type |
SRA |
| |
|
| Source name |
metastasis of cutaneous melanoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Metastatic melanoma clinical specimen
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
total RNA was extracted with qiagen RNeasy mini kit (cat# 74106) according to manufacturer protocol
libraries were constructed using Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) starting from 1µg of total RNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 13
hg18
|
| Data processing |
Basecalls performed using CASAVA version 1.9
Data were filtered using the Illumina quality control flag
Reads were aligned to the homo sapiens genome build hg19 using tophat (v2.0.8), which uses Bowtie (2.1.0) and Samtools (v0.1.18) using default parameters and --transcriptome H. sapiens index, UCSC hg19 gtf.
Raw read counts were summarised using HTSeq (v0.5.3p9), then normalized for library size differences using estimateSizeFactors function from DESeq package (v1.10.1).
Differential expression of genes was calculated with the same R package, using three biological replicas for each interference condition (shLuc and shKMT2D) for each MM patient.
Genome_build: hg19( samples 1-9); hg18( Samples 10-22)
Supplementary_files_format_and_content: list of differentially expressed genes between two conditions (shTINCR vs shSCR, samples 1-4) ; tab delimited text file containing normalized read counts for each gene ( samples 5-22)
|
| |
|
| Submission date |
Aug 15, 2016 |
| Last update date |
Nov 25, 2020 |
| Contact name |
Marine Melixetian |
| E-mail(s) |
[email protected]
|
| Organization name |
European Institute of Oncology
|
| Street address |
via Adamello 16
|
| City |
Milano |
| ZIP/Postal code |
20141 |
| Country |
Italy |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE85656 |
RNAseq analysis of lncRNA silenced primary melanoma cell line WM902B |
| GSE125835 |
Long non-coding RNA TINCR suppresses metastatic melanoma dissemination by preventing ATF4 translation |
|
| Relations |
| BioSample |
SAMN05578552 |
| SRA |
SRX2024375 |
