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Sample GSM5577902 Query DataSets for GSM5577902
Status Public on May 05, 2022
Title multi_PYMT_cd11b_hi_myeloid
Sample type SRA
 
Source name mammary ductal epithelium
Organism Mus musculus
Characteristics mouse model: MMTV-PyMT-mCherry-OVA
tumor type: spontaneous
tissue: mammary tumor
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 cd11b-hi-enriched Myeloid sort of spontaneous tumors from a pool of 4 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 SAMN21428599
SRA SRX12181729

Supplementary file Size Download File type/resource
GSM5577902_multi_PYMT_cd11b_hi_myeloid_raw_feature_bc_matrix.h5 33.3 Mb (ftp)(http) H5
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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