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Sample GSM2833285 Query DataSets for GSM2833285
Status Public on Jan 17, 2018
Title Naive CD8+ T Suv39h1-KO, rep1
Sample type SRA
 
Source name Suv39h1-KO
Organism Mus musculus
Characteristics infection status: Naive
cell type: CD8+ T cells
strain: C57BL/6
genotype: Suv39h1-KO
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 Suv39h1 -/-, 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 SAMN07840855
SRA SRX3337496

Supplementary file Size Download File type/resource
GSM2833285_Naive_KO_Rep1.h5 3.0 Mb (ftp)(http) H5
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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