|
| Status |
Public on Oct 12, 2019 |
| Title |
Sham_1_week |
| Sample type |
SRA |
| |
|
| Source name |
cardiac immune (CD45+) cells
|
| Organism |
Mus musculus |
| Characteristics |
condition: Sham
time point: 1_week
strain: C57BL/6J
|
| Extracted molecule |
total RNA |
| Extraction protocol |
~5,000 cells were loaded into one channel of the Single Cell Chip A for each sample using the Single Cell 3’ v2 single cell reagent kit (10X Genomics) for Gel bead Emulsion generation into the Chromium system. Following capture and lysis, we synthesized cDNA and amplified it for 14 cycles following the manufacturer’s protocol (10X Genomics). 50 ng of the amplified cDNA were then used for each sample to construct Illumina sequencing libraries.
Sequencing was performed on the NextSeq500 Illumina sequencing platform following 10x Genomics instruction for reads generation; at least 50.000 reads per cell were produced.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Sham_1_week_barcodes.tsv
Sham_1_week_genes.tsv
Sham_1_week_matrix.mtx
|
| Data processing |
Raw sequencing data (bcl-files) were converted to fastq files with Illumina bcl2fastq tool, integrated into the CellRanger (10X Genomics) suite (version 2.1.1).
The CellRanger analysis pipeline was used to generate a digital gene expression matrix staring from raw data.
The raw digital gene expression matrix (UMI counts per gene per cell) was imported in R (version 3.5.0) using Seurat R package (version Seurat_2.3.3)
The I1 contains the sample index. The R1 = cellular barcode (CB) (16 bp) + molecular barcode (MB) (umi) 10bp. The R2 contains the transcript read.
Genome_build: Pre-build mouse genome (version mm10-1.2.0) was used as genome reference.
Supplementary_files_format_and_content: UMI counts per gene per cell
Dataset1-Average-clusters-conditions.xlsx: Average of normalized gene expression values were obtained using Seurat AverageExpression function with default parameters.
Dataset2-Markers-clusters-conditions.xlsx: List of positive and negative markers specific to each cluster obtained with Seurat FindAllMarkers function with default parameters and min.pct=0.2.
|
| |
|
| Submission date |
Nov 26, 2018 |
| Last update date |
Oct 15, 2019 |
| Contact name |
Paolo Kunderfranco |
| E-mail(s) |
Paolo.Kunderfranco@humanitasresearch.it
|
| Organization name |
Humanitas Research Hospital
|
| Department |
Research
|
| Lab |
Bioinformatic Unit
|
| Street address |
Via Rita Levi Montalcini 4
|
| City |
Pieve Emanuele |
| State/province |
Milano |
| ZIP/Postal code |
20090 |
| Country |
Italy |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE122930 |
Single cell sequencing of mouse heart immune infiltrate in pressure overload-driven heart failure reveals extent of immune activation |
|
| Relations |
| BioSample |
SAMN10477310 |
| SRA |
SRX5063183 |
