|
| Status |
Public on Jan 17, 2018 |
| Title |
Naive CD8+ T cells WT, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
wild-type
|
| Organism |
Mus musculus |
| Characteristics |
infection status: Naive
cell type: CD8+ T cells
strain: C57BL/6
genotype: wild-type
|
| Growth protocol |
Naïve littermate and Suv39h1-KO CD8+ T cells, and day 7 post-infection Kb-OVA+ CD8+ T cells (from Listeria .m-OVA infected mice), were isolated by flowcytometry
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single-cell RNA-Seq libraries were prepared using Chromium Single Cell 3’ v2 Reagent Kit (10X Genomics) according to manufacturer’s protocol
Indexed sequencing libraries were constructed using the reagents from the Chromium Single Cell 3’ v2 Reagent Kit, following these steps: (1) fragmentation, end repair and A-tailing; (2) size selection with SPRI select; (3) adaptor ligation; (4) post ligation cleanup with SPRI select; (5) sample index PCR and cleanup with SPRI select beads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Wild-type, naive CD8 T cells, biological rep1
Raw data are multiplexed. Raw data consist of paired-end reads. Read1 includes the Chromium barcode while Read2 is the biological read sequence.
|
| Data processing |
quality control, Cell Ranger Single Cell Software Suite (v1.3.1)
sample de-multiplexing, Cell Ranger Single Cell Software Suite (v1.3.1)
barcode processing, Cell Ranger Single Cell Software Suite (v1.3.1)
single-cell 3′ gene counting , Cell Ranger Single Cell Software Suite (v1.3.1)
alignment, Cell Ranger Single Cell Software Suite (v1.3.1)
Genome_build: mm10
Supplementary_files_format_and_content: HDF5 Gene_Barcode Matrix files were generated using Cell Ranger Single Cell Software Suite (v1.3.1). For more information on the format and to read the matrix see : https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/h5_matrices. Technical replicates were aggregated using Cell Ranger Single Cell Software Suite (v1.3.1) command cellranger aggr.
|
| |
|
| Submission date |
Oct 27, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Luigia Pace |
| E-mail(s) |
Luigia.Pace@curie.fr
|
| Organization name |
Institut Curie
|
| Street address |
26 rue d'Ulm
|
| City |
Paris |
| ZIP/Postal code |
75005 |
| Country |
France |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE106264 |
single-cell-RNA-sequencing analysis of naive and Listeria monocytogenes-specific CD8+ T cells |
| GSE106268 |
single-cell-RNA-sequencing and H3K9me3 occupancy of CD8+ T cells |
|
| Relations |
| BioSample |
SAMN07840848 |
| SRA |
SRX3337495 |
