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Series GSE134284 Query DataSets for GSE134284
Status Public on Oct 29, 2020
Title CNS-Native Myeloid Cells Drive Immune Suppression in the Brain Metastatic Niche through Cxcl10
Organism Mus musculus
Experiment type Other
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 wild type C57Bl/6 mice to brain metastasis-associated myeloid cells (Br.MAM) from C57Bl/6 mice bearing E0771 brain metastases. In each sequencing round, we sequenced a total of four different mouse brains (2 naive and 2 metastasis-burdened). We created an antibody pool consisting of 6 different antibodies (CD45, CD25, CD3, CD4, CD11b, and CD86) 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 and later prepare one library consisting of all six samples and finally separate each sample in silico by it's unique hashing antibody.
 
Overall design Naïve brains were obtained from 2-3 month old female C57Bl/6 mice without brain metastases. Brains bearing metastases initiated by carotid injection of E0771 cells were obtained from 2-3 month old female mice (C57Bl/6) with established brain metastases (~2 weeks post injection). Cell suspensions were prepared by percoll gradient centrifugation enrichment to obtain suspensions enriched for immune cells. We created an antibody pool consisting of 6 different antibodies (CD45, CD25, CD3, CD4, CD11b, and CD86) 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 and later prepare one library consisting of all six samples and finally separate each sample in silico by it's unique hashing antibody.
 
Contributor(s) Zhang S, Guldner I
Citation(s) 33113353
Submission date Jul 15, 2019
Last update date Jan 30, 2021
Contact name Siyuan Zhang
E-mail(s) szhang8@nd.edu
Phone 574-631-4635
Organization name University of Notre Dame
Department Biological Sciences
Street address 1234 N. Notre Dame Ave
City South Bend
ZIP/Postal code 46617
Country USA
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (3)
GSM3941409 CITE-seq Met v Naïve mRNA/cDNA_2
GSM3941410 CITE-seq Met v Naïve ADT_2
GSM3941411 CITE-seq Met v Naïve HTO_2
This SubSeries is part of SuperSeries:
GSE134285 CNS-Native Myeloid Cells Drive Immune Suppression in the Brain Metastatic Niche through Cxcl10
Relations
BioProject PRJNA554648
SRA SRP214627

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE134284_CITE_counts.csv.gz 122.4 Kb (ftp)(http) CSV
GSE134284_RNA_counts.csv.gz 29.4 Mb (ftp)(http) CSV
GSE134284_meta.csv.gz 547.4 Kb (ftp)(http) CSV
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Raw data are available in SRA
Processed data are available on Series record

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