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SRX23925471: GSM8144250: 1NK-Control; Mus musculus; RNA-Seq
1 ILLUMINA (Illumina NovaSeq 6000) run: 32.6M spots, 9.8G bases, 3Gb downloads

External Id: GSM8144250_r1
Submitted by: Institute of bioorganic chemistry of the Russian Academy of Sciences
Study: Early transcriptomic response of innate immune cells to subcutaneous BCG vaccination of mice
show Abstracthide Abstract
Bacille Calmette-Guerin (BCG) vaccination might contribute to nonspecific enhancement of resistance to various infections. Thus, BCG in addition to the formation of specific immunity against mycobacteria is also capable of inducing “trained immunity” - the ability of the innate immune system to maintain the memory of past infections and use it to develop immune defenses against new ones. In this study, we performed RNA sequencing of innate immune cells derived from mice bone marrow and spleen three day after subcutaneous BCG vaccination to evaluate early transcriptomic response of innate immune cells Overall design: We performed RNA sequencing of innate immune cells derived from murine bone marrow and spleen three day after subcutaneous BCG vaccination. To do this, we obtained single-cell suspensions from the organs, stained the suspensions with conjugated anti-CD45, anti-CD11b, anti-NK1.1, anti-Ly6G, and anti-Ly6C antibodies, and subjected the suspen-sions 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+]. The samples were collected for each mouse from both control and BCG vaccinated groups. Monocytes and neutrophils were collected during sorting of bone marrow cell suspensions and NK-cells were collected from spleens. Then we have pre-pared double-indexed cDNA libraries for Illumina sequencing from the collected samples. The quality of the cDNA libraries was confirmed via Agilent Tape Station 2200 system, and the resulting cDNA library mix was subjected to NovaSeq 6000 sequencing. The RNA sequencing data was further processed with HISAT2 (GRCm38/mm10 was used as the reference genome), featureCount (GENCODE vM23, GRCm38.p6 was used as the reference transcriptome) and DESeq2 tools.
Sample: 1NK-Control
SAMN40420881 • SRS20735251 • All experiments • All runs
Organism: Mus musculus
Library:
Name: GSM8144250
Instrument: Illumina NovaSeq 6000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction 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.
Runs: 1 run, 32.6M spots, 9.8G bases, 3Gb
Run# of Spots# of BasesSizePublished
SRR2831683732,581,1629.8G3Gb2024-05-20

ID:
32230668

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