|
| Status |
Public on Sep 28, 2021 |
| Title |
RNA-seq_MPNST cell ST88-14 number 1 shHuR#1 |
| Sample type |
SRA |
| |
|
| Source name |
Cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: ST88-14
cell type: NF1-derived MPNST
genotype/variation: sh HuR
|
| Treatment protocol |
ST88-14 MPNST cells were infected with shControl or shHuR#1 lentivirus, selected with puromycin for 2 days, replated and then RNA isolated 2 days later
|
| Growth protocol |
Human MPNST cell line were maintained in Dulbecco’s modified Eagle Medium (DMEM) (Thermo Fisher Scientific) supplemented with 10% (v/v) fetal bovine serum (FBS) (Thermo Fisher Scientific) and 1% (v/v) antibiotic/antimycotic (Thermo Fisher Scientific) under standard conditions of 37 ºC and 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolated 2 days later with TRIzol Reagent (Thermo Fisher Scientific) following manufacturer’s instructions.
TruSeq® RNA Sample Preparation v2 (Illumina Inc.)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
shHuR3_1
shHuR3_vs_shCtrl_CountsxGene.txt
shHuR3_vs_shCtrl_CountsxIsoform.txt
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
Individual FASTQ files for each sample were merged prior to the quality control & filtering steps
Quality control of the reads was carried out using FASTQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were trimmed for adapters using cutadapt (Martin, 2011) and aligned to hg38 genome using STAR(Dobin et al., 2013).
Quantification in expected counts from genes and isoforms were computed by RSEM (Li and Dewey, 2011) using genecode annotation v.26 [https://www.gencodegenes.org/].
We use TMM method to estimate scale factors between samples followed by the voom function in limma to convert them into log2counts per million (logCPM).
Finally, differential expression between shControl and shHUR-infected cells were evaluated by LIMMA bioconductor package (Ritchie et al., 2015).
Genome_build: hg38
Supplementary_files_format_and_content: Tables of raw gene and isoform counts, obtained from the BAM files of the samples in each comparative. These tables are in tab separated plain text format.
|
| |
|
| Submission date |
Oct 01, 2018 |
| Last update date |
Sep 28, 2021 |
| Contact name |
Jose Luis Lavin |
| E-mail(s) |
joluito@gmail.com
|
| Organization name |
CIC bioGUNE
|
| Street address |
Parque Tecnológico de Bizkaia Building 502, Floor 0
|
| City |
Derio |
| State/province |
Bizkaia |
| ZIP/Postal code |
48160 |
| Country |
Spain |
| |
|
| Platform ID |
GPL15456 |
| Series (2) |
| GSE120685 |
The Role of the RNA-binding protein HuR in MPNST growth and metastasis [RNA-seq] |
| GSE120687 |
The Role of the RNA-binding protein HuR in MPNST growth and metastasis |
|
| Relations |
| BioSample |
SAMN10148350 |
| SRA |
SRX4779812 |
