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Sample GSM8331621

Query DataSets for GSM8331621

Status

Public on Jun 21, 2024

Title

1370824

Sample type

SRA

Source name

Prostate cancer-associated fibroblast

Organism

Homo sapiens

Characteristics

cell type: Prostate cancer-associated fibroblast

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted using RNeasy mini kit (Qiagen).
RNA integrity for library preparation was determined by analysis of extracted total RNA using a 2100 Bioanalyzer (Agilent Technologies) with RNA 6000 NanoChip. RNA concentrations were measured using Qubit RNA Assay Kit. Libraries were prepared from total RNA according to manufacturer instructions with Illumina Stranded mRNA Prep kit. Libraries quality was evaluated by size analysis on 2100 Bioanlyzer (Chip DNA HS) and concentrations were determined using Qubit DNA HS assay kit (Thermo Fisher Scientific).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq X Plus

Data processing

Reads preprocessing was performed by using fastp v0.20.0 applying specific parameters to remove residual adapter sequences and to keep only high-quality data (qualified_quality_phred=20, unqualified_percent_limit=30, average_qual=25, low_complexity_filter=True, complexity_threshold=30). The percentage of uniquely mapped reads resulted high with the mean value of 89% (mean value for sample: unmapped reads 6%, quality base >q30 90%). Then, passing filter reads were mapped to the genome reference (Homo sapiens) using STAR v2.7.0 with standard parameters, except for sjdbOverhang option set on read length. Genome and transcript annotations provided as input were downloaded from v105 of the Ensembl repository. Alignments were then elaborated by RSEM v1.3.3, to estimate transcript and gene abundances. Subsequently, the sample-specific gene-level abundances were merged into a single raw expression matrix by applying a dedicated RSEM command (rsem-generate-data-matrix). Genes with at least 10 counts in N samples were then selected, where N corresponds to the sample number in the smallest experimental group.
Assembly: Homo sapiens
Supplementary files format and content: tab-delimited includes raw counts for each sample

Submission date

Jun 16, 2024

Last update date

Jun 21, 2024

Contact name

Rosamaria Lappano

E-mail(s)

[email protected]

Organization name

University of Calabria

Street address

via P. Bucci