|
| Status |
Public on Mar 04, 2024 |
| Title |
47H1 treatment on collagen from patient 20961, sample 50 |
| Sample type |
SRA |
| |
|
| Source name |
monocyte-derived dendritic cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: monocyte-derived dendritic cells
patientid: 20961
treatment: anti-LAIR1
|
| Treatment protocol |
Generation of monocyte derived dendritic cells - Dendritic cells were derived from monocytes, which were purified from PBMCs using a human pan monocyte isolation kit (Miltenyi). DCs were generated by culturing monocytes in X-VIVO 15 media (Lonza) containing 50 ng/mL recombinant human GM-CSF (Peprotech) and 50 ng/mL recombinant human IL-4 (Peprotech) for 5-6 days. 96-well tissue culture plates (Corning) were coated with 5 µg/mL human collagen type 1 (Millipore Sigma) in PBS overnight at 4° C, then washed in PBS. 1 x 105 DCs were added to the plates with anti-LAIR1 or an isotype control antibody at the listed concentrations then incubated for 2 days at 37° C. Conditioned media was collected the next day and analyzed using Luminex (ProcartaPlex, ThermoFisher)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA isolation - RNA isoloation was perfomed using the RNEasy mini kit following manufacturer's instructions (Qiagen).
Sequencing - Total RNA was prepared for sequencing using the Illumina stranded mRNA library prep kit and sequenced on an Illumina NovaSeq SP V1 (100bp single-end reads and an average of 25 million reads were generated for each sample).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
For sequencing alignment, RNA-seq data raw reads were filtered using Trim Galore! (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove low quality and adaptor bases. Reads shorter than 20nt were discarded.
Mapping of filtered reads to UCSC hg19 genome sequences was performed using STAR (v2.6.0a). Counts were created using featureCounts (v1.6.2), and edgeR (v3.22.3) was used to generate normalized counts and execute DEG analysis.
Assembly: hg19
Supplementary files format and content: gene expression read counts in tabular format
|
| |
|
| Submission date |
Feb 29, 2024 |
| Last update date |
Mar 04, 2024 |
| Contact name |
Lee Benjamin Rivera |
| E-mail(s) |
lrivera@ngmbio.com
|
| Organization name |
NGM Bio
|
| Department |
Biology
|
| Street address |
333 Oyster Point Blvd.
|
| City |
South San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94080 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE260597 |
Anti-tumor activity of a novelLAIR1antagonist in combination with anti-PD-1to treat collagen-rich solid tumors (human) |
| GSE260599 |
Anti-tumor activity of a novelLAIR1antagonist in combination with anti-PD-1to treat collagen-rich solid tumors |
|
| Relations |
| BioSample |
SAMN40205019 |
| SRA |
SRX23797557 |
