|
| Status |
Public on Oct 29, 2019 |
| Title |
Isotype antibody [UN_241A] |
| Sample type |
SRA |
| |
|
| Source name |
Breast tumor single cell suspensions
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Breast tumor and immune infiltrates
strain: FVB/NJ
library construction: Chromium Single Cell 5’ Library Construction Kit (PN-1000020)
|
| Treatment protocol |
Mice were put on weekly antibody treatment regimen as soon as palpable tumors (200 mm^3) were detected
|
| Growth protocol |
HER2 expression was induced in mammary tissues of one month old mice, spontaneous breast tumor growth were monitored weekly
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Breast tumors were removed and processed into single cell suspensions as described in manuscript, and live singlet cells were sorted.
10X Genomics gene expression libraries were generated using Chromium Single Cell 5’ Library Construction Kit (PN-1000020). A targeted cell recovery of 4000 cells were used for each sample.
scRNA seq (10X Genomics), Single Cell 5' Gene Expression Libraries, 26x8x98 single i7 index. Sequenced on NovaSeq S4 (sample 1-10) and Hi Seq X (sample 11-13)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
4000-6000 live sorted single cells used per sample
|
| Data processing |
Fastq files for paired-end reads and the index file for each samples was procssed using 10X cellranger v 2.2.0 count program to generate an expressoin count matrix for each sample. Alignment was done to the GRCH38 for human transcripts and mm10 for the mouse transcripts.
The raw counts were analzed with Seurat v 2.3.4
Using Seurat the raw counts were normalized and scaled for each sample
The normalized counts were then combined for all samples and clustered using the standard Seurat workflow.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized Expresion Matrix
|
| |
|
| Submission date |
Oct 28, 2019 |
| Last update date |
Oct 29, 2019 |
| Contact name |
Zachary Conrad Hartman |
| E-mail(s) |
zch@duke.edu
|
| Phone |
919-684-9197
|
| Organization name |
Duke University
|
| Department |
Surgery
|
| Lab |
Lyerly Lab
|
| Street address |
Research Drive MSRB rm 414
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE139492 |
CD47 blockade augmentation of Trastuzumab antitumor efficacy dependent upon antibody-dependent-cellular-phagocytosis |
| GSE148482 |
Stimulation of oncogene-specific tumor infiltrating T-cells through combined vaccine and alpha-PD1 enable sustained anti-tumor responses against established HER2 breast cancer (BC) |
|
| Relations |
| BioSample |
SAMN13141082 |
| SRA |
SRX7064930 |
