|
| Status |
Public on Dec 06, 2022 |
| Title |
91_Macro-CSF1_CT |
| Sample type |
SRA |
| |
|
| Source name |
Macrophage
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: untreated
|
| Treatment protocol |
treated with recombinant human (rh)IL32β (100 ng/ml) for 24 hours
|
| Growth protocol |
Monocytes were obtained by elutriation and T cells were separated using anti-human CD3 magnetic beads. Monocyte-derived macrophages were differentiated with CSF1 (5 days).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with RNeasy Mini Kit (Qiagen) and sequenced on 3’ends
The libraries are prepared from 10 ng of total RNA in 4µl. The mRNA poly(A) tails are tagged with universal adapters, well-specific barcodes and unique molecular identifiers (UMIs) during template-switching reverse transcriptase. Barcoded cDNAs from multiple samples are then pooled, amplified and tagmented using a transposon-fragmentation approach which enriches for 3′ends of cDNA. A library of 350–800 bp length is run on an Illumina NovaSeq 6000 using NovaSeq 6000 SP Reagent Kit 100 cycles (ref #20027464)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Samples demultiplexing is performed with a python script. It will transform the raw paired-end fastq files into a single-end fastq file for each sample
Alignment on refseq reference transcriptome is performed using bwa
Aligned reads are parsed and UMI are counted for each gene in each sample to create an expression matrix
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Jul 07, 2021 |
| Last update date |
Dec 06, 2022 |
| Contact name |
David Chiron |
| E-mail(s) |
[email protected]
|
| Organization name |
CRCI2NA, INSERM_U1307, CNRS_6075, Nantes_Université
|
| Street address |
8 quai Moncousu
|
| City |
Nantes |
| ZIP/Postal code |
44000 |
| Country |
France |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE179636 |
The IL32/BAFF axis supports prosurvival dialog in the lymphoma ecosystem and is disrupted by NIK inhibition |
|
| Relations |
| BioSample |
SAMN20090398 |
| SRA |
SRX11369082 |
