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Status |
Public on Mar 19, 2023 |
Title |
id_53 - FAP - FOAM low |
Sample type |
SRA |
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Source name |
FAP
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Organism |
Homo sapiens |
Characteristics |
tissue: FAP treatment: None foam content: low class: FC-deprived precancerous intestinal lesions
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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.).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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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
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Submission date |
Mar 13, 2023 |
Last update date |
Mar 19, 2023 |
Contact name |
Giulio Ferrero |
Organization name |
University of Turin
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Department |
Dept. Clinical and Biological Sciences
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Street address |
Regione Gonzole, 10
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City |
Orbassano |
State/province |
TO |
ZIP/Postal code |
10043 |
Country |
Italy |
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Platform ID |
GPL18573 |
Series (1) |
GSE227206 |
Lipid engulfed macrophages interfere with protective T cell immunity and favor tumor progression in human colon carcinogenesis |
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Relations |
BioSample |
SAMN33737671 |
SRA |
SRX19650858 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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