|
| Status |
Public on Mar 01, 2020 |
| Title |
pH65_6 |
| Sample type |
SRA |
| |
|
| Source name |
cultured at pH 6.5
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: monocyte-derived dendritic cells
cultured with: M-CSF, IL-4 and TNF-a
condition: pH 6.5
|
| Treatment protocol |
Dendritic cells (CD1a+ CD16- cells) were sorted using an Aria cell sorter.
|
| Growth protocol |
Human CD14+ monocytes were cultured with M-CSF, IL-4 and TNF-a for 5 days, at pH 7.3 or pH 6.5 or in the presence of mTORC1 inhibitor Temsirolimus.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lyzed and mRNA extracted using Qiagen RNEasy Mini kit including on-column DNAse digestion.
cDNA was generated with SMART-Seq v4 Ultra Low Imput RNA Kit for Sequencing (Takara). Multiplexed pair-end libraries 100 nt in length were obtained using Nextera XT kit (Clontech).
Sequencing was performed in the same sequencing unit of NovaSeq (Illumina) (100-nt-length reads, paired end) with an average depth of 15 million reads per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
D245U17
|
| Data processing |
Quality of RNA-seq data was assessed using FastQC.
Reads were pseudo-aligned to the transcriptome using Salmon and transcript expression values were summarized using tximport.
Differential gene expression analysis was performed using DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: Count matrix (raw counts) was obtained using DESeq2.
|
| |
|
| Submission date |
Jan 06, 2020 |
| Last update date |
Mar 01, 2020 |
| Contact name |
Elodie Segura |
| E-mail(s) |
elodie.segura@curie.fr
|
| Phone |
+336156246720
|
| Organization name |
Institut Curie
|
| Department |
INSERM U932
|
| Street address |
26 rue d'Ulm
|
| City |
Paris |
| ZIP/Postal code |
75005 |
| Country |
France |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE143170 |
RNA-seq analysis of human monocyte-derived dendritic cells generated in vitro with M-CSF, IL-4 and TNF-a |
|
| Relations |
| BioSample |
SAMN13739601 |
| SRA |
SRX7505787 |
