|
| Status |
Public on Mar 07, 2024 |
| Title |
GD-MM_7 |
| Sample type |
SRA |
| |
|
| Source name |
peripheral blood
|
| Organism |
Homo sapiens |
| Characteristics |
cell purification: CD66b+CD10-CD11b+CD16+/dim cells isolated by flow cytometry sorting
cell type: Metamyelocytes purified from GCSF-treated donor
treatment: Freshly purified
|
| Treatment protocol |
freshly isolated cells
|
| Growth protocol |
Mononuclear cells and granulocytes were separated by density gradient centrifugation of the PB from GD, NSCLC/HNC patients or HDs onto either Ficoll-Paque or Biocoll under endotoxin-free conditions. LDNs/PMN-MDSCs were isolated from the mononuclear cell fraction, while NDNs were isolated from the granulocyte fraction, by either flow cytometry sorting or magnetic bead selection. Neutrophils precursors were purified from the mononuclear cell fraction from the PB of GDs by flow cytometry sorting.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted after cell lysis by the RNeasy Mini Kit (Qiagen, Venlo, Limburg, Netherlands). To completely remove any possible contaminating DNA, an on-column DNase digestion with the RNase-free DNase set (Qiagen) was performed during total RNA isolation.
Libraries for transcriptome analysis were prepared using Smart-seq2 protocol (PMID: 24056875)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were quality-filtered according the Illumina pipeline
Adapters and base quality trimming were performed using Trim Galore script with parameters -length 50 and -three_prime_clip_R1 3
Reads were mapped onto the Ensembl human transcriptome (version 94) with Hisat2 and quantified at the gene-level using HTSeq-count (-m intersection-nonempty -t exon -i gene_id)
Gene abundance was indicated as FPKM calculated according to the DESeq2 instruction.
Differential gene expression analysis and gene counts normalization among various samples was performed using DESeq2. Differentially expressed genes were identified by using as selection parameter an adjusted p-values (padj) lower than 0.05.
Genome_build: GrCh38 (Ensembl annotated transcriptome version 94)
Supplementary_files_format_and_content: Matrix of FPKM values for each sample
|
| |
|
| Submission date |
Dec 20, 2021 |
| Last update date |
Mar 07, 2024 |
| Contact name |
Barbara Mariotti |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Verona
|
| Department |
Medicine
|
| Lab |
Flavia Bazzoni
|
| Street address |
strada le grazie 8
|
| City |
Verona |
| State/province |
Verona |
| ZIP/Postal code |
37134 |
| Country |
Italy |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE191254 |
Surface CD52, CD84 and PTGER2 mark mature PMN-MDSCs from cancer patients and G-CSF-treated donors [bulk RNA-seq] |
| GSE250002 |
Surface CD52, CD84 and PTGER2 mark mature PMN-MDSCs from cancer patients and G-CSF-treated donors |
|
| Relations |
| BioSample |
SAMN24246826 |
| SRA |
SRX13455811 |
