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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 13, 2017 |
| Title |
BCGiv_HSC_2 |
| Sample type |
SRA |
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| Source name |
Hematopoietic stem cell
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| Organism |
Mus musculus |
| Characteristics |
mouse id: BCGiv_scs_2
treatment: BCG iv
tissue: Hematopoietic stem cell
infection status: Non Infected
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| Treatment protocol |
Throughout the paper, mice were intravenously (iv) or subcutaneously (sc) vaccinated with 1x106 singlesuspended BCG in 100μl PBS, unless otherwise indicated. Image stream analyses were used to identify what cells in the BM were infected with BCG. For the Mtb challenges, mice were either infected with ~50 CFU of Mtb H37Rv in a nose-only aerosol exposure unit (Intox), or with ~1000 CFU Mtb H37Rv via intratracheal instillation. BMDMs were derived as described previously (Coulombe et al., 2014) and infected with Mtb H37Rv at an MOI of 1.
C57BL/6J mice were sc or iv vaccinated with 1x106 singlesuspended BCG or iv PBSinjected. After four weeks, we generated BMDMs that were infected with H37Rv (MOI 0.5) and 0.5x106 cells were intratracheally transferred into naive Rag1-/- mice (Divangahi et al., 2009;; 2010). Parabiosis was performed as previously described (Ensan et al., 2016). Female CD45.1+ B6 mice were either PBSinjected or iv vaccinated with 1x106 singlesuspended BCGTice. After four weeks, CD45.1+ mice were joined to naive, female, weightmatched, and co-housed Ccr2-/- mice through skin suture and attachment of the front and hind legs. Six weeks post surgery the Ccr2-/- mice were intratracheally infected with H37Rv (~1000 CFU). CD45.1+ B6 mice were either PBS-injected or BCG iv-vaccinated (1x106 bacteria). After four weeks, BM cells were harvested and 4x106 cells were intravenously injected into CD45.2+ C57BL/6J mice 16 hours post irradiation with 9 Gy. Chimeric mice were aerosol infected with ~50 CFU Mtb H37Rv after 14 weeks when the hematopoietic compartment was reconstituted as determined by flow cytometry.
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| Growth protocol |
Six to ten-week old C57BL/6J, Rag1-/, Ccr2/-, and CD45.1+ B6 mice were purchased from Jackson Laboratories or bred at the RI-MUHC, Montreal, QC, Canada. All experiments were performed with male mice, except parabiosis, which was performed on female mice. All animal studies were conducted in accordance with the guidelines of and approved by the Animal Research Ethics Board of McGill University (project ID: 5860).
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-sequencing libraries were prepared using either the Illumina TruSeq protocol (for BMDMs) or the SMARTer® Stranded RNA-Seq Kit (for HSCs) and sequenced with single-end 100bp reads on an Illumina HiSeq2500.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Illumina bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to mm10 transcriptome (ENSEMBL v 81) using STAR
Gene-level expression estimates were calculated using featureCount (Liao et al., 2014).
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample ...
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| Submission date |
May 05, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Luis Barreiro |
| E-mail(s) |
lbarreiro@uchicago.edu
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| Organization name |
University of Chicago
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| Street address |
900 E 57th Street
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| City |
Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60637 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE98599 |
BCG reprogramming of hematopoietic stem cells generates protective innate immunity against tuberculosis (RNA-Seq) |
| GSE98600 |
BCG reprogramming of hematopoietic stem cells generates protective innate immunity against tuberculosis |
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| Relations |
| BioSample |
SAMN06895117 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2601617_BCGiv_BMDM_1_NI.Count.txt.gz |
196.8 Kb |
(ftp)(http) |
TXT |
| Raw data provided as supplementary file |
| Processed data provided as supplementary file |
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