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Sample GSM8144253 Query DataSets for GSM8144253
Status Public on May 20, 2024
Title 4NK-BCG
Sample type SRA
 
Source name Spleen
Organism Mus musculus
Characteristics tissue: Spleen
cell line: immune cells
cell type: NK cells (CD45+CD11-Nk1.1+)
genotype: wt
treatment: BCG
Growth protocol Mice were subcutaneously vaccinated with 10^6 CFU of Mycobacterium bovis/BCG in 100 µl phosphate-buffered saline, mice in the control group were subcutaneously injected with 100 µl of PBS. Three days after BCG administration, vaccinated and control animals were sacrificed under isoflurane anesthesia, by exsanguination and subsequent cervical dislocation, after which spleen and bone marrow were collected. Single-cell suspensions from the organs were stained with conjugated anti-CD45, anti-CD11b, anti-NK1.1, anti-Ly6G, and anti-Ly6C antibodies, and subjected the suspensions to fluorescence-activated cell sorting (FACS). The prepared cell suspensions were used for FACS sorting and three cell populations were collected: monocytes [CD45+CD11b+Ly6C+], neutrophils [CD45+CD11b+Ly6G+] and NK-cells [CD45+CD11b-NK1.1+]. Moreover, 1 million of total unsorted bone marrow cells from each mouse were collected. The samples were collected for each mouse from both control and BCG vaccinated groups.
Extracted molecule polyA RNA
Extraction protocol Harvested cells were lysed using ExtractRNA (Evrogen, Moscow, Russian Federation). RNA was extracted with RNA Clean & Concentrator TM-5 (Zymo Research, Irvine, CA, USA). To get rid of the excess ribosomal RNA, NEBNext rRNA Depletion Kit v2 was used.
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with Sample Puri-fication Beads (New England BioLabs) and a NEBNext Multiplex Oligos for Illumina (Unique Dual Index UMI Adaptors RNA Set 1, New England BioLabs) were used for the preparation of libraries.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing The raw reads were mapped on the murine reference genome (mm10) using HISAT2 (Galaxy Version 2.2.1+galaxy1)
The featureCounts tool (Galaxy Version 2.0.3+galaxy2) was used for counting reads to GENCODE release M23 annotated genes.
Assembly: mm10
Supplementary files format and content: .txt format, matrix table with featureCounts read counts
 
Submission date Mar 12, 2024
Last update date May 20, 2024
Contact name Liya Kondratyeva
E-mail(s) liakondratyeva@yandex.ru
Organization name Institute of bioorganic chemistry of the Russian Academy of Sciences
Street address Ulitsa Miklukho Maklaya, 16/10
City Moscow
ZIP/Postal code 117997
Country Russia
 
Platform ID GPL24247
Series (1)
GSE261448 Early transcriptomic response of innate immune cells to subcutaneous BCG vaccination of mice
Relations
BioSample SAMN40420878
SRA SRX23925474

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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