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Sample GSM5577904 Query DataSets for GSM5577904
Status Public on May 05, 2022
Title ortho_PYMT_bulk_myeloid
Sample type SRA
 
Source name mammary fat pad
Organism Mus musculus
Characteristics mouse model: C57BL/6
tumor type: orthotopically induced
tissue: mammary tumor
Growth protocol Cells were cultured at 37°C in DMEM containing 10% FCS/1% penicillin-streptomycin-glutamine. On the day of injection, cells were washed in PBS and 200 000 were injected in the mammary fat pat of female,
Extracted molecule polyA RNA
Extraction protocol Tumors from different stages were digested with collagenase IV and Dnase I for 30min, cells were filtered and pooled. Cells were stained 20min at 4°C with the antibody mix and myeloid cells were sorted in total or enriched for CD11b+ or CD11b- myeloid cells, according to CD45+CD90.2-B220-NK1.1-Ly6G-CD11b+ or CD11c.
After sorting, all cell preparations were pelleted and resuspended at 1x103cells/ml in 0.04%BSA/PBS and loaded onto the Chromium Controller (10X Genomics). Samples were processed for single-cell encapsulation and cDNA library generation using the Chromium Single Cell 3’v2 Reagent Kits (10X Genomics) according to manufacturer’s protocol. The library was subsequently sequenced on an Illumina HiSeq4000 (Illumina).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description Bulk Myeloid sort of orthotopically injected tumors from a pool of 5 mice
Data processing sequencer-generated bcl files were converted to fastqs using the cellranger mkfastq (cellranger version 3.0.2) command with default parameters.
fastq files were aligned to the mouse reference genome (with ENSEMBL v93 annotation) using cellranger count (cellranger version 3.0.2). This step also generated the submitted raw feature-barcode matrices
Genome_build: mm10
Supplementary_files_format_and_content: *raw_feature_bc_matrix.h5: raw count matrix from cellranger in the h5ad format;More information on 10X filetypes at https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices
 
Submission date Sep 14, 2021
Last update date May 05, 2022
Contact name Arjun Arkal Rao
E-mail(s) arjunarkal.rao@ucsf.edu
Organization name University of California, San Francisco
Department CoLabs
Lab Data Sciences CoLab
Street address 505 Parnassus Ave, S-447
City San Francisco
State/province CA
ZIP/Postal code 94143
Country USA
 
Platform ID GPL21103
Series (1)
GSE184096 Tumor-associated macrophage functional heterogeneity is driven by niche diversity in breast cancer
Relations
BioSample SAMN21428601
SRA SRX12181731

Supplementary file Size Download File type/resource
GSM5577904_ortho_PYMT_bulk_myeloid_raw_feature_bc_matrix.h5 48.2 Mb (ftp)(http) H5
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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