|
| Status |
Public on Oct 22, 2018 |
| Title |
Patient 4 Total Liver Homogenate |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Total Liver Homogenate
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The caudate lobe was cannulated with two or three 1.2-2mm diameter irrigation cannulae with olive tips, which were inserted into exposed vessels in the cut surface if the liver lobe (cannulae manufacturer: Ernst Kratz GmbH cat no: 1464LL, 1465LL). The lobe was flushed with HBS+EGTA at 4°C (perfusion rate of 10mL/min/cannulae), which removed any residual non-liver resident cells. Single cell isolation from the resected caudate liver lobe was performed with a modified “two-step” collagenase procedure6,97 as described in Fig. 1b. Eight to 12 million viable cells were recovered per gram of tissue as determined by Beckman Vi-Cell trypan blue exclusion. Viability for TLHs by trypan blue exclusion varied between 50-90% viable for the five livers profiled. Caudate lobes weighed on average 30.2 g +/-SD of 8.367g. TLHs were taken directly after dissociation for scRNA Seq.
10X Genomics Single Cell 3' v2 Reagent Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw sequencing data (bcl files) were converted to fastq files with Illumina bcl2fastq, version 2.19.1
The CellRanger (10X Genomics) secondary analysis pipeline was used to generate a digital gene expression matrix
Cells with a very small library size (< 1500) and a very high (> 0.5) mitochondrial genome transcript ratio were removed. Genes detected (UMI count > 0) in less than three cells were removed.
Normalization by scran R package
Clustering and Gene Expression Analysis by Seurat package
Genome_build: GRCh38
Supplementary_files_format_and_content: log2CPM gene expression values for filtered cells in CSV text format
|
| |
|
| Submission date |
Jun 07, 2018 |
| Last update date |
Oct 22, 2018 |
| Contact name |
Jeff Liu |
| E-mail(s) |
jeff.liu@utoronto.ca
|
| Phone |
416-340-4800
|
| Organization name |
University Health Network
|
| Department |
Princess Margaret Cancer Center
|
| Lab |
Zadeh Lab
|
| Street address |
101 College Street, RM 4-601
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 1L7 |
| Country |
Canada |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE115469 |
Dissecting the human liver cellular landscape by single cell RNA-seq reveals novel intrahepatic monocyte/ macrophage populations |
|
| Relations |
| BioSample |
SAMN09379682 |
| SRA |
SRX4180082 |
