|
| Status |
Public on Oct 29, 2020 |
| Title |
Healthy Control Lib_CGA-08_S8 |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral monocytes
|
| Organism |
Homo sapiens |
| Characteristics |
condition: Healthy Control individual
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Monocytes were enriched from Ficoll-isolated PBMCs by positive selection using CD14 Microbeads kit (Miltenyi Biotec), RNA was purified with the Direct-zol RNA Microprep or Miniprep Kit (Zymosan)
Total-RNA-sequencing library preparation was performed starting from 1 ng of total-RNA with the SMART-Seq Stranded Kit (Clontech-Takara). Libraries obtained were qualitatively assessed by using TapeStation 4200 (Agilent) and quantified by Qubit Fluorimeter (Thermo Fisher Scientific). Afterwards, they were multiplexed in equimolar pools and sequenced on a NextSeq-550 Illumina Platform generating at least 80 million 75-bp-PE reads per sample
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
Healthy Control
|
| Data processing |
Demultiplexing with “bcl2fastq2” Software (version 2.19.0)
Alignment with STAR (version 2.6.1)
Gene summarized counts were processed in R (version 3.5.2).Genes whose expression was major than 2 reads were filtered and vst normalized with the R package DESeq254 (version 1.22.2).
Genome_build: GRCh38 genome guided by GENCODE annotation (version 33)
|
| |
|
| Submission date |
Oct 28, 2020 |
| Last update date |
Oct 29, 2020 |
| Contact name |
sarah natalia mapelli |
| E-mail(s) |
sarah.mapelli@humanitasresearch.it
|
| Organization name |
Humanitas research
|
| Department |
Experimental Immunopathology
|
| Lab |
Experimental Immunopathology
|
| Street address |
Via Rita Levi Montalcini 4
|
| City |
Pieve Emanuele |
| State/province |
Milan |
| ZIP/Postal code |
20090 |
| Country |
Italy |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE160351 |
Macrophage expression and prognostic significance of the long pentraxin PTX3 in COVID-19 |
|
| Relations |
| BioSample |
SAMN16583816 |
| SRA |
SRX9390806 |
