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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 20, 2024 |
| Title |
2Bone Marrow-BCG |
| Sample type |
SRA |
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| Source name |
Bone Marrow
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| Organism |
Mus musculus |
| Characteristics |
tissue: Bone Marrow
cell line: Bone Marrow cells
cell type: Bone Marrow cells (unsorted)
genotype: wt
treatment: BCG
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| 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.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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
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| Submission date |
Mar 12, 2024 |
| Last update date |
May 20, 2024 |
| Contact name |
Liya Kondratyeva |
| E-mail(s) |
liakondratyeva@yandex.ru
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| Organization name |
Institute of bioorganic chemistry of the Russian Academy of Sciences
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| Street address |
Ulitsa Miklukho Maklaya, 16/10
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| City |
Moscow |
| ZIP/Postal code |
117997 |
| Country |
Russia |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE261448 |
Early transcriptomic response of innate immune cells to subcutaneous BCG vaccination of mice |
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| Relations |
| BioSample |
SAMN40420862 |
| SRA |
SRX23925490 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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