|
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).
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|
|
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
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|
|
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 |