|
| Status |
Public on Sep 27, 2023 |
| Title |
Partial Responder sample of Tumor liver (Mouse 1) |
| Sample type |
SRA |
| |
|
| Source name |
Liver containing metastases of CRC origin
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Liver containing metastases of CRC origin
condition: Partial Responder
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Liver metastases were isolated and dissociated into single cells by physical (chopping the tissue into small pieces) and enzymatic (collagenase, Dispase II and DNAse) digestion followed by a filtering step using a 0.4mm cell strainer. No antibody staining was performed, single cells were resuspended in autoMACS running buffer containing 7AAD (BioLegend/ 420404) in a 1/50 dilution. Viable cells were sorted based by gating on single 7AAD negative cells.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1, 10x Genomics, ref. CG000204). Briefly, sorted cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
|
| |
|
| Submission date |
Dec 19, 2022 |
| Last update date |
Sep 27, 2023 |
| Contact name |
Stefano Beretta |
| E-mail(s) |
beretta.stefano1@hsr.it
|
| Organization name |
San Raffaele Telethon Institute for Gene Therapy
|
| Street address |
Via Olgettina, 60
|
| City |
Milan |
| ZIP/Postal code |
20132 |
| Country |
Italy |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE221357 |
In vivo macrophage engineering reshapes the tumor microenvironment leading to eradication of liver metastases [scRNA-seq] |
| GSE221360 |
In vivo macrophage engineering reshapes the tumor microenvironment leading to eradication of liver metastases |
|
| Relations |
| BioSample |
SAMN32316013 |
| SRA |
SRX18777274 |
