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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 05, 2020 |
| Title |
Multi-modal single cell analysis reveals gut microbiota reshapes brain immune landscape in aged mouse model |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
We used CITE-seq (10x Gemoics-based) to profile and compare the transcriptomes and cell surface expression of a set of immune markers of naïve brain myeloid cells from young-adult (12 weeks old) wild type C57Bl/6 mice, aged (72 weeks old) wild type C57Bl/6 mice and young-adult and aged C57Bl/6 mice with antibiotics induced gut microbiota depletion. In one sequencing round, we sequenced a total of 12 different mouse brains (3 young control, 3 aged control, 3 young depleted gut microbiota (ABX) and 3 aged depleted gut microbiota (ABX)). We created an antibody pool consisting of 31 different antibodies (CCR2/CD192, C117/c-kit, CD11b, CD11c, CD172a/SIRPα, CD25, CD3, CD38, CD4, CD44, CD45, CD45R/B220, CD86, CD8a, CD90.1, Cx3cr1, F4/80, I-A/I-E, Ly6C, Ly6G, NK1.1, PD-1, PD-L1, CD169/Siglec-1, Siglec-H, TMEM119, XCR1, CD24, CD103, CD64, CD83) and stained each brain individually with this antibody pool. Then, we stained each brain with it's own unique hashing antibody so that we could subsequently pool the samples for loading onto the 10x Chromium. Young Control and Young ABX brains were tagged with HTOs 1-6 (HTO 1-3 for young control and HTO 4-6 for young ABX). Aged control and Aged ABX brains were tagged with HTOs 1-6 (HTO 1-3 for aged control and HTO 4-6 for aged ABX). Young and aged were loaded in separate wells on the 10X Chromium. The samples were tagged with unique nextera index primers to allow for preparation of one sequencing library consisting of all 12 samples and were separated in silico by it's unique hashing antibody and nextera index barcode combinations.
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| Overall design |
Naïve brains were obtained from twelve 12 week old female C57Bl/6 mice and twelve 72 week old female C57Bl/6 mice . Six young-adult and six aged mice received vehicle treatment and had an unperturbed gut microbiota and six young-adult and six aged mice received antibiotics treatment and had a depleted gut microbiota. All 24 brains (6 from each group) were individually processed into cell suspensions and collapsed into 12 final samples (3 young control, 3 aged control, 3 young depleted gut microbiota (ABX) and 3 aged depleted gut microbiota (ABX)). Cell suspensions were prepared by percoll gradient centrifugation enrichment to obtain suspensions enriched for immune cells. We created an antibody pool consisting of 31 different antibodies (CCR2/CD192, C117/c-kit, CD11b, CD11c, CD172a/SIRPα, CD25, CD3, CD38, CD4, CD44, CD45, CD45R/B220, CD86, CD8a, CD90.1, Cx3cr1, F4/80, I-A/I-E, Ly6C, Ly6G, NK1.1, PD-1, PD-L1, CD169/Siglec-1, Siglec-H, TMEM119, XCR1, CD24, CD103, CD64, CD83) and stained each brain individually with this antibody pool. Young Control and Young ABX brains were tagged with HTOs 1-6 (HTO 1-3 for young control and HTO 4-6 for young ABX). Aged control and Aged ABX brains were tagged with HTOs 1-6 (HTO 1-3 for aged control and HTO 4-6 for aged ABX). Young and aged were loaded in separate wells on the 10X Chromium. The samples were tagged with unique nextera index primers to allow for preparation of one sequencing library consisting of all 12 samples and were separated in silico by it's unique hashing antibody and nextera index barcode combinations.
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| Contributor(s) |
Zhang S, Golomb S |
| Citation(s) |
33264626 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 CA222405 |
Mechanisms of neuroinflammation in brain metastasis progression |
UNIVERSITY OF NOTRE DAME |
Siyuan Zhang |
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| Submission date |
Apr 06, 2020 |
| Last update date |
Dec 22, 2020 |
| Contact name |
Siyuan Zhang |
| E-mail(s) |
Siyuan.Zhang@UTSouthwestern.edu
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| Phone |
214-648-6537
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| Organization name |
UT Southwestern Medical Center
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| Department |
Department of Pathology
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| Street address |
6001 Forest Park Rd
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| City |
Dallas |
| ZIP/Postal code |
75235 |
| Country |
USA |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA623317 |
| SRA |
SRP255372 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE148127_ADT.counts.csv.gz |
335.2 Kb |
(ftp)(http) |
CSV |
| GSE148127_SCT.normalized.RNA.counts.csv.gz |
28.7 Mb |
(ftp)(http) |
CSV |
| GSE148127_TotalA_Ref.csv.gz |
878 b |
(ftp)(http) |
CSV |
| GSE148127_metadata.csv.gz |
568.7 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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