|
| Status |
Public on Oct 26, 2021 |
| Title |
SH-SY5Y WT sample 3 |
| Sample type |
SRA |
| |
|
| Source name |
Neuroblastoma cell line (SH-SY5Y)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Neuroblastoma cell line (SH-SY5Y)
genotype: Wild-type
|
| Treatment protocol |
Cells were transfected with a pCMV6-AC-GFP construct. Silencing of MINCR was obtained through siRNA-mediated silencing.
|
| Growth protocol |
The human neuroblastoma cell line SH-SY5Y (ATCC) was grown in DMEM supplemented with 15% fetal bovine serum, 1% L-Glutammine and 1% penicillin/streptomycin, at 37 °C in a 5% CO2 atmosphere.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were homogenized and total RNA was isolated by Trizol® reagent (Life Science Technologies, Italy) following the manufacturer’s specifications. RNAs were quantified using a Nanodrop ND-100 Spectrophotometer (Nanodrop Technologies, Wilmington, USA) and a 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit, Waldbronn, Germany); RNAs with a 260:280 ratio of ≥1.5 and an RNA integrity number of ≥8 were subjected to deep sequencing.
SENSE Total RNA-Seq Library Prep Kit (Lexogen) using 500 ng total RNA and sequenced by Illumina NextSeq 550 sequencer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
FastQ files were generated via llumina bcl2fastq2 Version 2.17.1.14
Gene and transcript intensities were computed using STAR/RSEM software using GRCh38 (Gencode release 27) as a reference, using the “-strandness forward” option. Differential expression analysis for mRNA and lncRNA was performed using R package DESeq2
Genome_build: HG19
Supplementary_files_format_and_content: counts,FPKM,TPM
|
| |
|
| Submission date |
Sep 03, 2021 |
| Last update date |
Oct 26, 2021 |
| Contact name |
Maria Garofalo |
| E-mail(s) |
maria.garofalo01@universitadipavia.it
|
| Organization name |
IRCCS Mondino Foundation
|
| Lab |
Genomic and Post Genomic Unit
|
| Street address |
Via Mondino 2
|
| City |
Pavia |
| ZIP/Postal code |
27100 |
| Country |
Italy |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE183410 |
MINCR: a Long non-coding RNA shared between cancer and neurodegeneration |
|
| Relations |
| BioSample |
SAMN21216942 |
| SRA |
SRX12009382 |
