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Sample GSM7093187

Query DataSets for GSM7093187

Status

Public on Mar 19, 2023

Title

id_13 - Cancer - FOAM low

Sample type

SRA

Source name

CRC

Organism

Homo sapiens

Characteristics

tissue: CRC
treatment: None
foam content: low
class: FC depleted CRC stage (I or II)

Extracted molecule

total RNA

Extraction protocol

RNA was harvested using Maxwell RSC miRNA tissue kit on Maxwell RSC Instrument (Promega). The RNA concentration was assessed with a Qubit 4 fluorometer (ThermoFisher). RNA purity was assessed as 260/280 and 269/230 ratios by spectometric analysis and RNA quality was verified on a 2100 bioanalyzer (Agilent Techn.).
200-800 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared with the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit (Illumina Inc.).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NextSeq 500

Data processing

Sequencing reads were preprocessed with fastp v0.21.0 (Chen et al., 2018) in default settings to remove reads associated with a low quality (phred quality <Q15), shorter than 15 nt reads, or with more than 5 Ns.
Reads passing the filtering step were aligned to the human Gencode v36 transcriptome using Salmon v1.4.0 (Patro et al., 2017) with option --validateMappings, --seqBias, and --gcBias.
Gene expression levels were normalized using tximport v.1.18 while DESeq2 v1.30.1 was applied for the differential expression analysis
Assembly: hg38
Supplementary files format and content: TPM-normalized gene expression levels

Submission date

Mar 13, 2023

Last update date

Mar 19, 2023

Contact name

Giulio Ferrero

Organization name

University of Turin

Department

Dept. Clinical and Biological Sciences

Street address

Regione Gonzole, 10