230127_VH00228_144_AAAGNCJHV_AllSamples

This dataset contains the first sequencing series of all the samples libraries described below. The dataset 230601_VH00228_181_AAAGNF7HV_AllSamples contains the second sequencing series of the same samples libraries The dataset VH00228_144_AAAGNCJHV_181_AAAGNF7HV_AllAggregations contains the aggregations of the resequenced libraries. The dataset VH00228_144_AAAGNCJHV_181_AAAGNF7HV_AllMerges contains the merges of the various conditions and timepoints. Description of the samples preparation : To establish a high-resolution immune atlas of healthy prostate and prostate cancer we performed scRNA-seq on sorted tissue-resident CD45+ immune cells from the inducible adult PTEN(i)pe-/- mice at the Prostatic Intraepithelial Neoplasia stage (PIN) and Adenocarcinoma stages, and age-matched healthy PTENL2/L2 control mice at 3 months and 9 months post-tamoxifen administration respectively. A few minutes prior sacrifice, mice were injected intravenously with fluorescent anti-CD45.2 antibodies to perform blood/tissue partitioning, allowing to exclude cells present in the vasculature and ensure to study solely of the immune cells present in prostate parenchyma. Cells were extracted from DLV prostate lobes by enzymatic digestion. Prostate samples from three PTEN(i)pe−/− mice at 3 months post-tamoxifen were pooled prior to sorting. Similarly, prostate samples from five sex-matched PTENL2/L2 control littermates at 3 months post-tamoxifen were also pooled prior to sorting. The same approach was applied for the 9 months samples of PTEN(i)pe−/− and control mice respectively. Tissue resident CD45+ immune cells were sorted by fluorescence-activated cell sorting (FACS). As we found previously that neutrophils were prevalent within the leukocyte infiltrate from PIN to adenocarcinoma stages of Pten(i)pe−/−prostate, neutrophils were sorted separately from the other CD45+ immune cells and cells were mixed again at a ratio of 25% neutrophils to 75% CD45+ non-neutrophil immune cells prior 10X Genomics Chromium System encapsulation and scRNA sequencing. We included 8 independent samples encompassing 2 replicates of PtenL2/L2 control at 3 months, PtenL2/L2 control at 9 months, Pten(i)pe−/− at 3 months PIN and Pten(i)pe−/− at 9 months adenocarcinoma. Details on the samples libraries : 230127_VH00228_144_AAAGNCJHV_CTRL3mo_1 | Mus Musculus Prostate Control 3 months post tam Replicate 1 Sequencing Run 1 | PTENL2/L2 | 3 mo Tamoxifen | WT prostate (mouse age: 5 months) 230127_VH00228_144_AAAGNCJHV_CTRL3mo_2 | Mus Musculus Prostate Control 3 months post tam Replicate 2 Sequencing Run 1 | PTENL2/L2 | 3 mo Tamoxifen | WT prostate (mouse age: 5 months) 230127_VH00228_144_AAAGNCJHV_CTRL9mo_1 | Mus Musculus Prostate Control 9 months post tam Replicate 1 Sequencing Run 1 | PTENL2/L2 | 9 mo Tamoxifen | WT prostate (mouse age: 11 months) 230127_VH00228_144_AAAGNCJHV_CTRL9mo_2 | Mus Musculus Prostate Control 9 months post tam Replicate 2 Sequencing Run 1 | PTENL2/L2 | 9 mo Tamoxifen | WT prostate (mouse age: 11 months) 230127_VH00228_144_AAAGNCJHV_PTEN3mo_1 | Mus Musculus Prostate PIN 3 months post tam Replicate 1 Sequencing Run 1 | PTEN(i)pe−/− | 3 mo Tamoxifen | Tumor prostate at PIN stage (mouse age: 5 months) 230127_VH00228_144_AAAGNCJHV_PTEN3mo_2 | Mus Musculus Prostate PIN 3 months post tam Replicate 2 Sequencing Run 1 | PTEN(i)pe−/− | 3 mo Tamoxifen | Tumor prostate at PIN stage (mouse age: 5 months) 230127_VH00228_144_AAAGNCJHV_PTEN9mo_1 | Mus Musculus Prostate Adenocarcinoma 9 months post tam Replicate 1 Sequencing Run 1 | PTEN(i)pe−/− | 9 mo Tamoxifen | Tumor prostate at Adenocarcinoma stage (mouse age: 11 months) 230127_VH00228_144_AAAGNCJHV_PTEN9mo_2 | Mus Musculus Prostate Adenocarcinoma 9 months post tam Replicate 2 Sequencing Run 1 | PTEN(i)pe−/− | 9 mo Tamoxifen | Tumor prostate at Adenocarcinoma stage (mouse age: 11 months)