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| Status |
Public on Oct 29, 2020 |
| Title |
CNS-Native Myeloid Cells Drive Immune Suppression in the Brain Metastatic Niche through Cxcl10 [R07_CCR2Cx3cr1B] |
| Organism |
Mus musculus |
| Experiment type |
Other
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| Summary |
We performed CITE-seq (10x Genomics-based) to profile and compare the transcriptomes and cell surface expression of immune epitopes in the brains and blood of different transgenic mice (Cx3cr1+/-; Cx3cr1-/-; CCR2+/-; CCR2-/-) during homeostasis or brain metastasis. We sequenced a total of eight different samples. We created an antibody pool consisting of 35 different antibodies and stained each sample individually with this antibody pool. Then, we stained each sample with it's own unique hashing antibody so that we could subsequently pool the samples for loading onto the 10x Chromium and later prepare one library consisting of all sight samples and finally separate each sample in silico by it's unique hashing antibody. The samples are as follows: (1) HTO1: brain of naïve CCR2+/- mouse; (2) HTO2: brain of naïve CCR2+/- mouse; (3) HTO3: brain of naïve CCR2-/- mouse; (4) HTO4: brain of naive CCR2-/-; (5) HTO5: blood of naïve Cx3cr1+/- mouse; (6) HTO6: blood of metastasis-burdened Cx3cr1+/- mouse; (7) HTO7: blood of naïve Cx3cr1-/- mouse; (8) HTO8: blood of metastasis-burdened Cx3cr1-/- mouse.The following sample comparisons were made: HTO1 and HTO2 versus HTO3 and HTO4; HTO5 versus HTO7; HTO6 versus HTO8.
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| Overall design |
Naïve brains and blood were obtained from 2-3 month old female Cx3cr1+/-, Cx3cr1-/-, CCR2+/-, or CCR2-/- mice without brain metastases. Blood from brain metastasis-bearing mice initiated by carotid injection of E0771 cells were obtained from 2-3 month old female mice of the aforementioned genotypes with established brain metastases (~2 weeks post injection). Cell suspensions were prepared by percoll gradient centrifugation enrichment to obtain suspensions enriched for immune cells from the brain, and whole blood was RBC-lysed and then pelleted for peripheral blood samples. We created an antibody pool consisting of 35 different antibodies and stained each sample individually with this antibody pool. Then, we stained each sample with it's own unique hashing antibody so that we could subsequently pool the samples for loading onto the 10x Chromium and later prepare one library consisting of all eight samples and finally separate each sample in silico by it's unique hashing antibody.
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| Contributor(s) |
Zhang S, Guldner I |
| Citation(s) |
33113353 |
| Submission date |
Nov 05, 2019 |
| Last update date |
Jan 30, 2021 |
| Contact name |
Siyuan Zhang |
| E-mail(s) |
szhang8@nd.edu
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| Phone |
574-631-4635
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| Organization name |
University of Notre Dame
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| Department |
Biological Sciences
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| Street address |
1234 N. Notre Dame Ave
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| City |
South Bend |
| ZIP/Postal code |
46617 |
| Country |
USA |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (3) |
| GSM4150648 |
CITE-seq mRNA/cDNA [CCR2_Cx3cr1B_SI-GA-G11] |
| GSM4150649 |
CITE-seq ADT [CCR2_Cx3cr1B_ADT-RPI-1] |
| GSM4150650 |
CITE-seq HTO [CCR2_Cx3cr1B_HTO_Nextera_i7_UDP01] |
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| This SubSeries is part of SuperSeries: |
| GSE134285 |
CNS-Native Myeloid Cells Drive Immune Suppression in the Brain Metastatic Niche through Cxcl10 |
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| Relations |
| BioProject |
PRJNA587760 |
| SRA |
SRP228491 |
