|
Status |
Public on Nov 13, 2016 |
Title |
naive B cells replicate3 |
Sample type |
SRA |
|
|
Source name |
lymphocytes_naive B cells
|
Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 Stage: 8 weeks after immunization cell type: sorted B cells from spleen cell subtype: naive B cells
|
Extracted molecule |
total RNA |
Extraction protocol |
Spleen cells were isolated and all mononuclear cells were stained with a combination of antibodies (anti-CD19, anti-IgM, anti-IgG). Then subsets of memory B cells were sorted as CD19+HEL+YFP+IgM+ or IgG+ and naive cells as CD19+HEL+YFP-IgM+ using a FACSAriaIII flow cytometer. The purity of the sorted populations varied from 90-95%. Directional libraries were prepared using the TruSeq Stranded total RNA Sample preparation kit following the manufacturer’s instructions (Illumina). The libraries were quantified by fluorimetric measurements with the Qubit® dsDNA HS Assay Kit (ThermoFisher). 51-bp Single Read sequences were generated on the Hiseq2500 sequencer according to manufacturer’s instructions (Illumina). Sequences were demultiplexed using the Illumina pipeline (Gerald, included in CASAVA version 1.7) giving FASTQ formatted reads.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
AF9-Nai1
|
Data processing |
cleaning with clean_ngs (v 0.7) alignment with tophat (v 1.4.1.1) counting with htseq-count (v 0.6.1) Genome_build: GRCm38 (Ensembl version 74) Supplementary_files_format_and_content: Htseq-count file; txt file with name of gene and corresponding counting
|
|
|
Submission date |
Mar 29, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Rachel Legendre |
E-mail(s) |
rachel.legendre@pasteur.fr
|
Organization name |
Institut Pasteur
|
Department |
Research and Resource Center for Scientific Informatics
|
Lab |
Hub of Bioinformatics and Biostatistics
|
Street address |
28, rue du docteur Roux
|
City |
Paris |
ZIP/Postal code |
75724 |
Country |
France |
|
|
Platform ID |
GPL17021 |
Series (1) |
GSE79672 |
Comparison of gene expression of memory B cells subpopulations |
|
Relations |
BioSample |
SAMN04589344 |
SRA |
SRX1668193 |