General Information
- Experiment ID
- OEX014925
- Experiment Name
- Single-cell multiomics
- Experiment Type
- Transcriptomic single cell
- Description
- Single-cell multiomics sequencing analysis of cells freshly dissociated from prostate tumors with independent replicates at different cancer progression stages (Figures 1B and S1D), which enabled the joint profiling of chromatin accessibility and gene expression in the same individual cell.
- Protocol
- The prostates of T2PPRC mice were dissected and minced with scissors. The dissociated prostate cells were resuspended in Red Blood Cell Lysis Solution (Miltenyi Biotec, no. 130-094-183) and incubated at room temperature for 2 min. Dead cells were removed with Dead Cell Removal Kit (Miltenyi Biotec, no. 130-090-101), and the cells were counted via the Countess II FL Automated Cell Counter (Thermo Fisher Scientific). Cells were lysed on ice for 5 min. Isolated nuclei from T2PPRC mouse prostates cells were transposed and loaded onto the Chromium Next GEM Chip J (10X Genomics). Then, the chip with prostate cells was loaded on a Chromium Controller. The library was constructed according to the manufacturer’s instructions. Fifteen mouse prostate samples with different barcodes were run on a NovaSeq6000 (Illumina) (To overcome the limitation of 4.5 months as the lifespan for TPPRC mice due to probable lesions of other organs, we grafted 4.5-month prostate tumors under renal capsule of SCID mice for another 1.5 months to achieve total time of 6 months).
Experiment information
- Attributes
-
library_layout Paired mate_pair n/a insertion_size n/a number_of_reads_sequenced n/a library_name n/a library_selection PCR library_strategy RNA-Seq platform Illumina NovaSeq 6000 - Project
-
1
Project ID Project name Create Date OEP002972 Single-cell multiomics reveals the dynamics of pioneer forces driving prostate cancer lineage plasticity 2021-12-09 - Samples
-
7
Sample ID Sample Name Organism Tissue Create Date OES128954 Wild type Mus musculus prostate 2021-12-12 OES128955 M1 Mus musculus prostate 2021-12-12 OES128957 M2.5 Mus musculus prostate 2021-12-12 OES128952 W2 Mus musculus prostate 2021-12-12 OES128958 M3.5 Mus musculus prostate 2021-12-12 OES128959 M4.5 Mus musculus prostate 2021-12-12 OES128953 M6 Mus musculus prostate 2021-12-12 - Runs
-
14
Run ID Run Name Sample Data Num Create Date OER236990 scRNA-seq WT Wild type 8 2021-12-12 OER236997 scATAC-seq M1 M1 32 2021-12-12 OER236998 scATAC-seq M2.5 M2.5 64 2021-12-12 OER236999 scATAC-seq W2 W2 32 2021-12-12 OER237000 scATAC-seq M3.5 M3.5 32 2021-12-12 OER237001 scATAC-seq M4.5 M4.5 32 2021-12-12 OER237002 scATAC-seq M6 M6 16 2021-12-12 OER237004 scRNA-seq M1 M1 8 2021-12-12 OER237005 scRNA-seq M2.5 M2.5 16 2021-12-12 OER237006 scRNA-seq W2 W2 8 2021-12-12 OER237007 scRNA-seq M3.5 M3.5 8 2021-12-12 OER237008 scRNA-seq M4.5 M4.5 12 2021-12-12 OER237009 scRNA-seq M6 M6 4 2021-12-12 OER237010 scATAC-seq WT Wild type 32 2021-12-12 - Analysis
-
15
Analysis ID Analysis Title Analysis Type Data Num Create Date OEZ008173 SC-multiomics cellranger-arc outs (Wild type-1) Other 0 2021-12-12 OEZ008176 SC-multiomics cellranger-arc outs (Wild type-2) Other 0 2021-12-12 OEZ008177 SC-multiomics cellranger-arc outs (W2-1) Other 0 2021-12-12 OEZ008178 SC-multiomics cellranger-arc outs (W2-2) Other 0 2021-12-12 OEZ008179 SC-multiomics cellranger-arc outs (M1-1) Other 0 2021-12-12 OEZ008180 SC-multiomics cellranger-arc outs (M1-2) Other 0 2021-12-12 OEZ008181 SC-multiomics cellranger-arc outs (M2.5-1) Other 0 2021-12-12 OEZ008182 SC-multiomics cellranger-arc outs (M2.5-2) Other 0 2021-12-12 OEZ008183 SC-multiomics cellranger-arc outs (M3.5-1) Other 0 2021-12-12 OEZ008184 SC-multiomics cellranger-arc outs (M3.5-2) Other 0 2021-12-12 OEZ008186 SC-multiomics cellranger-arc outs (M4.5-1) Other 0 2021-12-12 OEZ008187 SC-multiomics cellranger-arc outs (M4.5-2) Other 0 2021-12-12 OEZ008188 SC-multiomics cellranger-arc outs (M6) Other 0 2021-12-12 OEZ008190 SC-multiomics cellranger-arc outs (M2.5-3) Other 0 2021-12-12 OEZ008191 SC-multiomics cellranger-arc outs (M2.5-4) Other 0 2021-12-12
Author Information
- Create Date
- 2021-12-12
- Last Modified
- 2022-08-28
- Submission
- Fei Li
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences